Methods
* (Bio::FlatFileIndex::Results)
+ (Bio::Sequence::Common)
+ (Bio::FlatFileIndex::Results)
<< (Bio::FlatFileIndex::Indexer::NameSpaces)
<< (Bio::Sequence::Common)
<< (Bio::Alignment::OriginalAlignment)
<=> (Bio::PDB::Residue)
<=> (Bio::Location)
<=> (Bio::PDB::Record::ATOM)
<=> (Bio::Map::Mapping)
<=> (Bio::PDB::Model)
<=> (Bio::PDB::Chain)
== (Bio::GFF::GFF2::Record)
== (Bio::Blast::NCBIOptions)
== (Bio::FlatFileIndex::Flat_1::Record)
== (Bio::GFF::GFF3::Record::Target)
== (Bio::GFF::GFF2::Record::Value)
== (Bio::GFF::GFF3::Record::Gap)
== (Bio::GFF::GFF2::MetaData)
== (Bio::GFF::GFF3::SequenceRegion)
== (Bio::Alignment::OriginalAlignment)
Pdb_LString (Bio::PDB::DataType::ConstLikeMethod)
Pdb_Real (Bio::PDB::DataType::ConstLikeMethod)
Pdb_String (Bio::PDB::DataType::ConstLikeMethod)
[] (Bio::Feature)
[] (Bio::NucleicAcid::Data)
[] (Bio::FlatFileIndex::FileIDs)
[] (Bio::PDB::Model)
[] (Bio::PDB)
[] (Bio::PDB::Residue)
[] (Bio::AminoAcid::Data)
[] (Bio::FlatFile::AutoDetect)
[] (Bio::FastaNumericFormat)
[] (Bio::FlatFile::AutoDetect::RuleTemplate)
[] (Bio::PhyloXML::Parser)
[] (Bio::Locations)
[] (Bio::AAindex2)
[] (Bio::PDB::DataType::Pdb_LString)
[] (Bio::PDB::DataType::Pdb_String)
[] (Bio::FlatFileIndex::BDBwrapper)
[] (Bio::PDB::DataType::Pdb_Real)
[] (Bio::CodonTable)
[] (Bio::Features)
[] (Bio::PDB::Coordinate)
[] (Bio::CodonTable)
[] (Bio::PDB::Chain)
[] (Bio::FANTOM::MaXML::Sequences)
[] (Bio::FANTOM::MaXML::Annotations)
[] (Bio::Alignment::OriginalAlignment)
[]= (Bio::FlatFileIndex::FileIDs)
[]= (Bio::CodonTable)
[]= (Bio::FlatFileIndex::BDBwrapper)
[]= (Bio::Registry::DB)
__output_phylip_common (Bio::Alignment::Output)
__store__ (Bio::Alignment::OriginalAlignment)
aa (Bio::AminoAcid::Data)
aa (Bio::Sequence)
aalen (Bio::KEGG::GENES)
aalen (Bio::GenPept)
aalen (Bio::FastaFormat)
aalen (Bio::SPTR)
aalen (Bio::NBRF)
aaseq (Bio::DBGET)
aaseq (Bio::PDB::Chain)
aaseq (Bio::GenPept)
aaseq (Bio::SPTR)
aaseq (Bio::GCG::Seq)
aaseq (Bio::KEGG::GENES)
aaseq (Bio::FastaFormat)
aaseq (Bio::NBRF)
ab (Bio::MEDLINE)
absent_count= (Bio::PhyloXML::BinaryCharacters)
absolute (Bio::Locations)
abstract (Bio::MEDLINE)
ac (Bio::PROSITE)
ac (Bio::TRANSFAC)
ac (Bio::EMBLDB::Common)
acc2hit (Bio::Hinv)
acc_version (Bio::FastaFormat)
acc_version (Bio::FastaDefline)
acc_version (Bio::NCBIDB::Common)
acceptor_score (Bio::Genscan::Report::Exon)
accession (Bio::FastaFormat)
accession (Bio::Iprscan::Report::Match)
accession (Bio::NCBIDB::Common)
accession (Bio::EMBLDB::Common)
accession (Bio::FastaDefline)
accession (Bio::PDB)
accessions (Bio::FastaFormat)
accessions (Bio::EMBLDB::Common)
accessions (Bio::FastaDefline)
accessions (Bio::NCBIDB::Common)
accessions (Bio::Sequence)
acos (Bio::PDB::Utils)
activity (Bio::KEGG::DRUG)
ad (Bio::MEDLINE)
adapter (Bio::Sequence)
add (Bio::FlatFile::AutoDetect)
add (Bio::FlatFileIndex::Indexer::NameSpaces)
add (Bio::FlatFileIndex::FileIDs)
add (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
addAtom (Bio::PDB::Residue)
addChain (Bio::PDB::Model)
addLigand (Bio::PDB::Chain)
addModel (Bio::PDB)
addResidue (Bio::PDB::Chain)
addSolvent (Bio::PDB::Model)
add_attribute (Bio::GFF::GFF2::Record)
add_continuation (Bio::PDB::Record)
add_cut_range (Bio::RestrictionEnzyme::Range::SequenceRange)
add_cut_ranges (Bio::RestrictionEnzyme::Range::SequenceRange)
add_cuts_from_cut_ranges (Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts)
add_defline (Bio::FastaDefline)
add_edge (Bio::Tree)
add_exclusive (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
add_header_line (Bio::Blat::Report)
add_header_line (Bio::Fastq)
add_horizontal_cut_range (Bio::RestrictionEnzyme::Range::SequenceRange)
add_line (Bio::Blat::Report)
add_line (Bio::Fastq)
add_mapping_as_map (Bio::Map::ActsLikeMap)
add_mapping_as_marker (Bio::Map::ActsLikeMarker)
add_node (Bio::Tree)
add_nr (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
add_options (Bio::Blast::NCBIOptions)
add_overwrite (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
add_record (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
add_secondary_namespaces (Bio::FlatFileIndex::Indexer::Parser::TemplateParser)
add_seq (Bio::Alignment::OriginalAlignment)
add_sequences (Bio::Alignment::OriginalAlignment)
add_spacing (Bio::RestrictionEnzyme::StringFormatting)
add_taxon (Bio::Nexus::TaxaBlock)
add_taxon (Bio::Nexus::DataBlock)
add_to_leaves (Bio::KEGG::Taxonomy)
add_to_path (Bio::KEGG::Taxonomy)
add_to_tree (Bio::KEGG::Taxonomy)
add_token (Bio::Nexus::GenericBlock)
add_tree (Bio::Nexus::TreesBlock)
add_tree_name (Bio::Nexus::TreesBlock)
addindex_bdb (Bio::FlatFileIndex::Indexer)
addindex_flat (Bio::FlatFileIndex::Indexer)
adjacency_matrix (Bio::Tree)
adjacent_nodes (Bio::Tree)
affiliations (Bio::MEDLINE)
aldh2 (Bio::Shell::Demo)
alias_list (Bio::KEGG::Keggtab)
aliases (Bio::KEGG::Keggtab)
align (Bio::Sim4::Report::Hit)
align (Bio::Spidey::Report::Hit)
align (Bio::MAFFT::Report)
align (Bio::ClustalW::Report)
align (Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands)
align_len (Bio::Sim4::Report::SegmentPair)
align_len (Bio::Blat::Report::SegmentPair)
align_with_cuts (Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands)
aligned_strands (Bio::RestrictionEnzyme::DoubleStranded)
aligned_strands_with_cuts (Bio::RestrictionEnzyme::DoubleStranded)
alignment (Bio::Phylip::PhylipFormat)
alignment (Bio::MAFFT::Report)
alignment (Bio::Alignment::MultiFastaFormat)
alignment (Bio::ClustalW::Report)
alignment (Bio::GCG::Msf)
alignment_collect (Bio::Alignment::EnumerableExtension)
alignment_collect (Bio::Alignment::HashExtension)
alignment_collect (Bio::Alignment::OriginalAlignment)
alignment_concat (Bio::Alignment::HashExtension)
alignment_concat (Bio::Alignment::EnumerableExtension)
alignment_length (Bio::Alignment::EnumerableExtension)
alignment_lstrip! (Bio::Alignment::EnumerableExtension)
alignment_normalize! (Bio::Alignment::EnumerableExtension)
alignment_rstrip! (Bio::Alignment::EnumerableExtension)
alignment_site (Bio::Alignment::EnumerableExtension)
alignment_slice (Bio::Alignment::EnumerableExtension)
alignment_strip! (Bio::Alignment::EnumerableExtension)
alignment_subseq (Bio::Alignment::EnumerableExtension)
alignment_window (Bio::Alignment::EnumerableExtension)
alink (Bio::DBGET)
all (Bio::Shell::Demo)
all_reac (Bio::KEGG::ENZYME)
alt= (Bio::PhyloXML::Point)
altid (Bio::FANTOM::MaXML::Sequence)
always_check= (Bio::FlatFileIndex::DataBank)
always_check_consistency (Bio::FlatFileIndex)
always_check_consistency= (Bio::FlatFileIndex)
ancestors (Bio::Tree)
annotations (Bio::FANTOM::MaXML::Sequence)
append (Bio::Features)
append (Bio::Feature)
append (Bio::References)
append (Bio::Pathway)
append_hsp (Bio::HMMER::Report::Hit)
applies_to= (Bio::PhyloXML::Property)
array_to_string (Bio::Nexus::Util)
ask_yes_or_no (Bio::Shell::Core)
assoc (Bio::Feature)
at_content (Bio::Sequence::NA)
at_skew (Bio::Sequence::NA)
atom_seq (Bio::PDB::Chain)
atoms (Bio::PDB::AtomFinder)
attribute (Bio::GFF::GFF2::Record)
attributes_to_hash (Bio::GFF::GFF2::Record)
au (Bio::MEDLINE)
author (Bio::LITDB)
author (Bio::AAindex)
authors (Bio::MEDLINE)
authors (Bio::PDB)
auto (Bio::Sequence)
auto (Bio::FlatFile)
auto (Bio::Sequence)
auto (Bio::AAindex)
autodetect (Bio::FlatFile)
autodetect (Bio::FlatFile)
autodetect (Bio::FlatFile::AutoDetect)
autodetect_file (Bio::FlatFile)
autodetect_flatfile (Bio::FlatFile::AutoDetect)
autodetect_io (Bio::FlatFile)
autodetect_stream (Bio::FlatFile)
ba (Bio::TRANSFAC::MATRIX)
basecount (Bio::GenBank)
bc (Bio::TRANSFAC::GENE)
bdb_open (Bio::FlatFileIndex::DataBank)
bellman_ford (Bio::Pathway)
bf (Bio::TRANSFAC::MATRIX)
bf (Bio::TRANSFAC::CLASS)
bf (Bio::TRANSFAC::SITE)
bfind (Bio::DBGET)
bfs (Bio::Pathway)
bfs_shortest_path (Bio::Pathway)
bget (Bio::DBGET)
bibitem (Bio::Reference)
bibtex (Bio::Reference)
binfo (Bio::DBGET)
bioflat_dir (Bio::Shell::Core)
bit_score (Bio::Blast::Report::Hit)
bit_score (Bio::Blast::Default::Report::Hit)
bit_score (Bio::Fasta::Report::Hit)
blast (Bio::FastaFormat)
blink (Bio::DBGET)
block_count (Bio::Blat::Report::Hit)
block_it (Bio::SiRNA::ShRNA)
block_sizes (Bio::Blat::Report::Hit)
blocks (Bio::Blat::Report::Hit)
blue= (Bio::PhyloXML::BranchColor)
blunt? (Bio::RestrictionEnzyme::DoubleStranded)
bman (Bio::DBGET)
bootstrap= (Bio::Tree::Node)
bootstrap_string= (Bio::Tree::Node)
both_intron (Bio::Sim4::Report::SegmentPair)
breadth_first_search (Bio::Pathway)
bref (Bio::DBGET)
bs (Bio::TRANSFAC::FACTOR)
bs (Bio::TRANSFAC::GENE)
btab (Bio::DBGET)
btit (Bio::DBGET)
c2s (Bio::Sequence::NA::MidiTrack)
cache_all (Bio::FlatFileIndex::FileIDs)
calc_checksum (Bio::GCG::Seq)
calculatePlane (Bio::PDB::Utils)
call_command (Bio::Command)
call_command_fork (Bio::Command)
call_command_open3 (Bio::Command)
call_command_popen (Bio::Command)
callback (Bio::Command::Tmpdir)
cc (Bio::PROSITE)
cc (Bio::EMBL)
cc (Bio::SPTR)
cc (Bio::TRANSFAC)
cc_web_resource (Bio::SPTR)
cd (Bio::TRANSFAC::CELL)
cdna_rep_h_invitational (Bio::Hinv::HitDefinition)
cdna_splicing_isoform_curation (Bio::Hinv::HitDefinition)
cds_start (Bio::FANTOM::MaXML::Annotations)
cds_stop (Bio::FANTOM::MaXML::Annotations)
cdsfeatures (Bio::SQL::Sequence)
cell (Bio::Reference)
centreOfGravity (Bio::PDB::Utils)
chains (Bio::PDB::ChainFinder)
check (Bio::FlatFileIndex::FileIDs)
check (Bio::FlatFileIndex::FileID)
check_all (Bio::FlatFileIndex::FileIDs)
check_consistency (Bio::FlatFileIndex)
check_consistency (Bio::FlatFileIndex::DataBank)
check_marshal (Bio::Shell::Ghost)
check_options (Bio::Meme::Mast)
check_ruby_version (Bio::Shell::Setup)
chi_square (Bio::ContingencyTable)
chi_square_element (Bio::ContingencyTable)
child_nodes (Bio::KEGG::Keggtab)
children (Bio::Tree)
chose_sort_proc (Bio::FlatFileIndex::Indexer)
chromosome (Bio::KEGG::GENES)
chromosomes (Bio::KEGG::GENOME)
circular (Bio::GenBank)
circular (Bio::GenPept)
cl (Bio::TRANSFAC::CLASS)
cl (Bio::TRANSFAC::FACTOR)
classes (Bio::KEGG::ENZYME)
classification (Bio::GenBank)
classification (Bio::PDB)
clean_all (Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts)
clear (Bio::Tree)
clear_node (Bio::Tree)
clear_relations! (Bio::Pathway)
clique (Bio::Pathway)
cliquishness (Bio::Pathway)
cloneids (Bio::FANTOM::MaXML::Sequences)
close (Bio::FlatFileIndex::DataBank)
close (Bio::FlatFileIndex::NameSpaces)
close (Bio::FlatFileIndex::BDBwrapper)
close (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
close (Bio::FlatFileIndex::FileID)
close (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
close (Bio::PhyloXML::Parser)
close (Bio::FlatFile)
close (Bio::FlatFileIndex)
close (Bio::FlatFileIndex::Template::NameSpace)
close (Bio::FlatFile::BufferedInputStream)
close (Bio::FlatFileIndex::FileIDs)
close! (Bio::Command::Tmpdir)
close_all (Bio::FlatFileIndex::FileIDs)
close_all (Bio::FlatFileIndex::NameSpaces)
close_flatfile (Bio::FlatFileIndex::Indexer::Parser::TemplateParser)
close_history (Bio::Shell::Ghost)
closed? (Bio::FlatFileIndex)
closing_splash (Bio::Shell::Ghost)
cn (Bio::TRANSFAC::FACTOR)
co (Bio::TRANSFAC::GENE)
codes (Bio::Sequence::AA)
codon_usage (Bio::Sequence::NA)
codon_usage (Bio::KEGG::GENES)
cofactors (Bio::KEGG::ENZYME)
collect! (Bio::Alignment::OriginalAlignment)
collect_align (Bio::Alignment::OriginalAlignment)
collect_each_site (Bio::Alignment::EnumerableExtension)
collect_edge! (Bio::Tree)
collect_node! (Bio::Tree)
colors (Bio::Shell::Core)
cols (Bio::AAindex2)
column_sum (Bio::ContingencyTable)
column_sum_all (Bio::ContingencyTable)
commands (BiorubyController)
comment (Bio::KEGG::GLYCAN)
comment (Bio::AAindex)
comment (Bio::EMBL)
comment (Bio::PROSITE)
comment (Bio::KEGG::GENOME)
comment (Bio::TRANSFAC)
comment (Bio::NCBIDB::Common)
comment (Bio::KEGG::ENZYME)
comment (Bio::KEGG::COMPOUND)
comment (Bio::KEGG::DRUG)
comment (Bio::FastaFormat)
comment= (Bio::SQL::Sequence)
comment_only? (Bio::GFF::GFF2::Record)
comments (Bio::GFF::Record)
comments (Bio::GFF::GFF2::Record)
comments (Bio::SQL::Sequence)
comments= (Bio::GFF::GFF2::Record)
comments= (Bio::GFF::Record)
common_name (Bio::NCBIDB::Common)
common_subgraph (Bio::Pathway)
compact (Bio::Alignment::OriginalAlignment)
compact (Bio::KEGG::Taxonomy)
compact! (Bio::Alignment::OriginalAlignment)
compcheck (Bio::GCG::Msf)
complement (Bio::RestrictionEnzyme::Fragments)
complement (Bio::Sequence::NA)
complement (Bio::RestrictionEnzyme::DoubleStranded::CutLocations)
complement (Bio::Location)
complement (Bio::SangerChromatogram)
complement! (Bio::Sequence::NA)
complement! (Bio::SangerChromatogram)
complement? (Bio::Sim4::Report::Hit)
complement? (Bio::Spidey::Report::Hit)
complement_to_array_index (Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation)
composition (Bio::KEGG::GLYCAN)
composition (Bio::Sequence::Common)
compounds (Bio::KEGG::GLYCAN)
concat (Bio::Sequence::Common)
concat (Bio::Alignment::OriginalAlignment)
concat (Bio::Tree)
conect (Bio::PDB::ChemicalComponent)
confidence= (Bio::PhyloXML::ProteinDomain)
confidence= (Bio::PhyloXML::Events)
confidence= (Bio::PhyloXML::Events)
config (Bio::Meme::Mast)
config_color (Bio::Shell::Ghost)
config_echo (Bio::Shell::Ghost)
config_file (Bio::Shell::Core)
config_message (Bio::Shell::Ghost)
config_pager (Bio::Shell::Ghost)
config_show (Bio::Shell::Ghost)
config_splash (Bio::Shell::Ghost)
configure (Bio::Shell::Ghost)
consensus_each_site (Bio::Alignment::EnumerableExtension)
consensus_iupac (Bio::Alignment::SiteMethods)
consensus_iupac (Bio::Alignment::EnumerableExtension)
consensus_string (Bio::Alignment::EnumerableExtension)
consensus_string (Bio::Alignment::SiteMethods)
contains_marker? (Bio::Map::ActsLikeMap)
contingency_coefficient (Bio::ContingencyTable)
continue? (Bio::PDB::Record)
continue? (Bio::PDB::Record)
control_avg (Bio::KEGG::EXPRESSION)
control_sd (Bio::KEGG::EXPRESSION)
control_var (Bio::KEGG::EXPRESSION)
converged? (Bio::Blast::Default::Report)
converged? (Bio::Blast::Default::Report::Iteration)
convert (Bio::TogoWS::REST)
convert (Bio::TogoWS::REST)
convert_match (Bio::Alignment::EnumerableExtension)
convert_nothing (Bio::Sequence::QualityScore::Converter)
convert_scores_from_phred_to_solexa (Bio::Sequence::QualityScore::Converter)
convert_scores_from_solexa_to_phred (Bio::Sequence::QualityScore::Converter)
convert_to_xyz (Bio::PDB::Utils)
convert_unmatch (Bio::Alignment::EnumerableExtension)
copy (Bio::CodonTable)
correlation_coefficient (Bio::AAindex1)
count (Bio::NCBI::REST::ESearch::Methods)
cp (Bio::TRANSFAC::FACTOR)
crc64 (Bio::Iprscan::Report::Match)
create (Bio::FlatFileIndex::Flat_1::Record)
create_action_at (Bio::RestrictionEnzyme::DoubleStranded)
create_bins (Bio::RestrictionEnzyme::Range::SequenceRange)
create_config_file (Bio::PAML::Codeml)
create_control_file (Bio::PAML::Codeml)
create_cut_locations (Bio::RestrictionEnzyme::DoubleStranded)
create_definition_hash (Bio::PDB::Record)
create_enzyme_actions (Bio::RestrictionEnzyme::Analysis)
create_flat_dir (Bio::Shell::Ghost)
create_primary_and_complement (Bio::RestrictionEnzyme::DoubleStranded)
create_real_dir (Bio::Shell::Ghost)
create_save_dir (Bio::Shell::Ghost)
create_save_dir_ask (Bio::Shell::Ghost)
cu_list (Bio::KEGG::GENES)
current (Bio::Reference)
custom_raise (Bio::SOFT)
cut (Bio::RestrictionEnzyme::Analysis)
cut (Bio::RestrictionEnzyme::Analysis)
cut (Bio::RestrictionEnzyme)
cut_and_return_by_permutations (Bio::RestrictionEnzyme::Analysis)
cut_symbol (Bio::RestrictionEnzyme::CutSymbol::CutSymbol__)
cut_symbol (Bio::RestrictionEnzyme::CutSymbol)
cut_symbol= (Bio::RestrictionEnzyme::CutSymbol::CutSymbol__)
cut_with_enzyme (Bio::Sequence::NA)
cut_with_enzymes (Bio::Sequence::NA)
cut_without_permutations (Bio::RestrictionEnzyme::Analysis)
cut_without_permutations (Bio::RestrictionEnzyme::Analysis)
data (Bio::FastaNumericFormat)
data (Bio::Abif)
data_class (Bio::EMBL)
data_dir (Bio::Shell::Core)
data_source (Bio::FANTOM::MaXML::Annotations)
data_source (Bio::KEGG::GENOME)
data_source_coverage (Bio::Hinv::HitDefinition)
data_source_db_reference_protein_motif_id (Bio::Hinv::HitDefinition)
data_source_definition (Bio::Hinv::HitDefinition)
data_source_homologous_species (Bio::Hinv::HitDefinition)
data_source_identity (Bio::Hinv::HitDefinition)
data_source_similarity_category (Bio::Hinv::HitDefinition)
database (Bio::KEGG::Keggtab)
database (Bio::SQL::Sequence)
database_desc (Bio::SQL::Sequence)
database_description (Bio::Blast::Remote::Information)
databases (Bio::Blast::Remote::Information)
databases (Bio::Fetch)
datasrc (Bio::FANTOM::MaXML::Annotation)
datatype= (Bio::PhyloXML::Property)
date (Bio::PROSITE)
date (Bio::TRANSFAC)
date (Bio::GenBank)
date (Bio::GenPept)
date (Bio::MEDLINE)
date (Bio::Iprscan::Report::Match)
date_created (Bio::EMBL)
date_modified (Bio::EMBL)
date_modified (Bio::GenBank)
db (Bio::Registry)
db (Bio::Blast::Default::Report)
db (Bio::Blast::WU::Report)
db_by_abbrev (Bio::KEGG::Keggtab)
db_ids (Bio::GO::External2go)
db_len (Bio::Blast::Report)
db_num (Bio::Blast::Report)
db_path (Bio::KEGG::Keggtab)
db_path_by_abbrev (Bio::KEGG::Keggtab)
dbclass= (Bio::FlatFile)
dbclasses (Bio::FlatFile::AutoDetect::RuleProc)
dbclasses (Bio::FlatFile::AutoDetect::RuleRegexp)
dbget (Bio::DBGET)
dblinks (Bio::EMBL)
dblinks (Bio::KEGG::COMPOUND)
dblinks (Bio::KEGG::GLYCAN)
dblinks (Bio::KEGG::ENZYME)
dblinks (Bio::AAindex)
dblinks (Bio::KEGG::ORTHOLOGY)
dblinks (Bio::KEGG::DRUG)
dblinks (Bio::KEGG::GENES)
dblinks_as_hash (Bio::KEGG::ORTHOLOGY)
dblinks_as_hash (Bio::KEGG::Common::DblinksAsHash)
dblinks_as_hash (Bio::KEGG::ENZYME)
dblinks_as_hash (Bio::KEGG::GLYCAN)
dblinks_as_hash (Bio::KEGG::DRUG)
dblinks_as_hash (Bio::KEGG::GENES)
dblinks_as_hash (Bio::KEGG::COMPOUND)
dblinks_as_strings (Bio::KEGG::GLYCAN)
dblinks_as_strings (Bio::KEGG::ENZYME)
dblinks_as_strings (Bio::KEGG::GENES)
dblinks_as_strings (Bio::KEGG::ORTHOLOGY)
dblinks_as_strings (Bio::KEGG::DRUG)
dblinks_as_strings (Bio::KEGG::COMPOUND)
dbref (Bio::PDB)
dbs (Bio::GO::External2go)
dbsource (Bio::GenPept)
ddbj (Bio::Blast::Remote)
de (Bio::EMBLDB::Common)
de (Bio::TRANSFAC::GENE)
de (Bio::TRANSFAC::MATRIX)
de (Bio::PROSITE)
de (Bio::TRANSFAC::SITE)
def_rec (Bio::PDB::Record)
default (Bio::FlatFile::AutoDetect)
default= (Bio::FlatFile::AutoDetect)
default_email (Bio::NCBI)
default_email= (Bio::NCBI)
default_namespaces (Bio::FlatFileIndex)
default_namespaces= (Bio::FlatFileIndex)
default_parser (Bio::PSORT::PSORT2::Report)
default_parser (Bio::PSORT::PSORT1::Report)
default_tool (Bio::NCBI)
default_tool= (Bio::NCBI)
definition (Bio::KEGG::GENOME)
definition (Bio::Spidey::Report::Hit)
definition (Bio::KEGG::GENES)
definition (Bio::KEGG::REACTION)
definition (Bio::AAindex)
definition (Bio::PDB)
definition (Bio::SQL::Sequence)
definition (Bio::NCBIDB::Common)
definition (Bio::Blat::Report::Hit)
definition (Bio::Blast::Default::Report::Hit)
definition (Bio::PROSITE)
definition (Bio::KEGG::ORTHOLOGY)
definition (Bio::EMBLDB::Common)
definition (Bio::Sim4::Report::Hit)
definition= (Bio::SQL::Sequence)
delete (Bio::SQL::Sequence)
delete (Bio::Alignment::OriginalAlignment)
delete (Bio::Blast::NCBIOptions)
delete (Bio::Pathway)
delete_attribute (Bio::GFF::GFF2::Record)
delete_attributes (Bio::GFF::GFF2::Record)
delete_entry_accession (Bio::SQL)
delete_entry_id (Bio::SQL)
depth_first_search (Bio::Pathway)
descendents (Bio::Tree)
description (Bio::EMBLDB::Common)
description (Bio::SQL::Sequence)
description (Bio::Iprscan::Report::Match)
description (Bio::FastaDefline)
description= (Bio::SQL::Sequence)
descriptions (Bio::FastaDefline)
design (Bio::SiRNA)
design (Bio::SiRNA::ShRNA)
dfs (Bio::Pathway)
dfs (Bio::KEGG::Taxonomy)
dfs_topological_sort (Bio::Pathway)
dfs_with_level (Bio::KEGG::Taxonomy)
dihedral_angle (Bio::PDB::Utils)
dijkstra (Bio::Pathway)
directed (Bio::Pathway)
directed? (Bio::Pathway)
direction (Bio::Fasta::Report::Hit)
disease (Bio::KEGG::GENOME)
diseases (Bio::KEGG::ENZYME)
distance (Bio::PDB::Coordinate)
distance (Bio::PDB::Utils)
distance (Bio::Tree)
distance= (Bio::PhyloXML::CladeRelation)
distance= (Bio::PhyloXML::SequenceRelation)
distance= (Bio::Tree::Edge)
distance_matrix (Bio::Tree)
distance_string= (Bio::Tree::Edge)
divent (Bio::PSORT::PSORT2::Report)
division (Bio::EMBL)
division (Bio::SQL::Sequence)
division (Bio::GenPept)
division (Bio::PROSITE)
division (Bio::KEGG::GENES)
division (Bio::GenBank)
division= (Bio::SQL::Sequence)
dna (Bio::Sequence::NA)
dna (Bio::DAS)
dna! (Bio::Sequence::NA)
do_align (Bio::Alignment::OriginalAlignment)
do_parse (Bio::PDB::Record)
do_parse (Bio::PDB::Record::ATOM)
doi (Bio::MEDLINE)
donor_score (Bio::Genscan::Report::Exon)
down_regulated (Bio::KEGG::EXPRESSION)
dp (Bio::MEDLINE)
dr (Bio::SPTR)
dr (Bio::PROSITE)
dr (Bio::TRANSFAC::FACTOR)
dr (Bio::TRANSFAC::SITE)
dr (Bio::TRANSFAC::CLASS)
dr (Bio::EMBLDB::Common)
dt (Bio::TRANSFAC)
dt (Bio::SPTR)
dt (Bio::PROSITE)
dt (Bio::EMBL)
dump_list (Bio::Pathway)
dump_matrix (Bio::Pathway)
dump_parameters (Bio::PAML::Common)
dup (Bio::Alignment::OriginalAlignment)
duplications= (Bio::PhyloXML::Events)
each (Bio::FastaNumericFormat)
each (Bio::Blat::Report::Hit)
each (Bio::Meme::Mast::Report)
each (Bio::REBASE)
each (Bio::DAS::ENTRY_POINT)
each (Bio::FANTOM::MaXML::Annotations)
each (Bio::Blast::Fastacmd)
each (Bio::Blast::Report)
each (Bio::Blast::Report::Iteration)
each (Bio::FlatFileIndex::Results)
each (Bio::Blast::Report::Hit)
each (Bio::Blast::Default::Report)
each (Bio::HMMER::Report::Hit)
each (Bio::HMMER::Report)
each (Bio::PDB::Residue)
each (Bio::Blast::Default::Report::Hit)
each (Bio::FANTOM::MaXML::Sequences)
each (Bio::Blat::Report)
each (Bio::Fasta::Report)
each (Bio::PDB)
each (Bio::References)
each (Bio::Alignment::OriginalAlignment)
each (Bio::PDB::Model)
each (Bio::FlatFileIndex::Indexer::Parser::TemplateParser)
each (Bio::CodonTable)
each (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
each (Bio::Spidey::Report::Hit)
each (Bio::Sim4::Report)
each (Bio::FlatFile)
each (Bio::Spidey::Report)
each (Bio::Sim4::Report::Hit)
each (Bio::Blast::Default::Report::Iteration)
each (Bio::FlatFileIndex::FileIDs)
each (Bio::PhyloXML::Parser)
each (Bio::PDB::Chain)
each (Bio::Features)
each (Bio::Feature)
each (Bio::Locations)
each_atom (Bio::PDB::AtomFinder)
each_atom (Bio::PDB::Residue)
each_cds (Bio::GenBank)
each_cds (Bio::EMBL)
each_chain (Bio::PDB::ChainFinder)
each_chain (Bio::PDB::Model)
each_edge (Bio::Tree)
each_edge_in_path (Bio::Tree)
each_entry (Bio::FlatFile)
each_entry (Bio::Blast::Fastacmd)
each_files (Bio::FlatFileIndex::NameSpaces)
each_gene (Bio::EMBL)
each_gene (Bio::GenBank)
each_hetatm (Bio::PDB::HetatmFinder)
each_heterogen (Bio::PDB::HeterogenFinder)
each_heterogen (Bio::PDB::Chain)
each_hit (Bio::HMMER::Report)
each_hit (Bio::Spidey::Report)
each_hit (Bio::Blast::Report)
each_hit (Bio::Sim4::Report)
each_hit (Bio::Blast::Default::Report)
each_hit (Bio::Blat::Report)
each_hsp (Bio::HMMER::Report::Hit)
each_iteration (Bio::Blast::Report)
each_iteration (Bio::Blast::Default::Report)
each_model (Bio::PDB)
each_motif (Bio::Meme::Mast::Report)
each_names (Bio::FlatFileIndex::NameSpaces)
each_node (Bio::Tree)
each_out_edge (Bio::Tree)
each_pair (Bio::Alignment::OriginalAlignment)
each_residue (Bio::PDB::ResidueFinder)
each_residue (Bio::PDB::Chain)
each_rule (Bio::FlatFile::AutoDetect)
each_seq (Bio::Alignment::OriginalAlignment)
each_seq (Bio::Alignment::HashExtension)
each_seq (Bio::Alignment::EnumerableExtension)
each_seq (Bio::Alignment::ArrayExtension)
each_site (Bio::Alignment::EnumerableExtension)
each_site_step (Bio::Alignment::EnumerableExtension)
each_symbol (Bio::PDB::Record)
each_window (Bio::Alignment::EnumerableExtension)
each_with_index (Bio::FlatFileIndex::FileIDs)
eclinks (Bio::KEGG::GENES)
edge (Bio::KEGG::KGML::Relation)
edges (Bio::Pathway)
edges (Bio::Tree)
efetch (Bio::PubMed)
efetch (Bio::NCBI::REST)
efetch (Bio::PubMed)
efetch (Bio::NCBI::REST)
eff_space (Bio::Blast::Report)
einfo (Bio::NCBI::REST)
einfo (Bio::NCBI::REST)
el (Bio::TRANSFAC::SITE)
elements (Bio::FlatFile::AutoDetect)
elements (Bio::PDB::Coordinate)
embl (Bio::Reference)
encode (Bio::Sequence::NA::MidiTrack)
end (Bio::Hinv::KeywordSearch)
endnote (Bio::Reference)
entret (Bio::EMBOSS)
entrez_query (Bio::Blast::Report)
entries (Bio::Alignment::MultiFastaFormat)
entropy (Bio::Blast::Report)
entropy (Bio::Blast::Default::Report)
entry (Bio::KEGG::ENZYME)
entry (Bio::KEGG::GENES)
entry (Bio::TogoWS::REST)
entry (Bio::SPTR)
entry (Bio::TogoWS::REST)
entry (Bio::Shell::Demo)
entry (Bio::FastaFormat)
entry (Bio::Blast::Report::BlastXmlSplitter)
entry (Bio::EMBL)
entry (Bio::NBRF)
entry_database_list (Bio::TogoWS::REST)
entry_database_list (Bio::TogoWS::REST)
entry_ended_pos (Bio::Blast::Report::BlastXmlSplitter)
entry_ended_pos (Bio::FlatFile)
entry_id (Bio::PROSITE)
entry_id (Bio::GenPept)
entry_id (Bio::LITDB)
entry_id (Bio::PDB::ChemicalComponent)
entry_id (Bio::MEDLINE)
entry_id (Bio::KEGG::GENOME)
entry_id (Bio::KEGG::ENZYME)
entry_id (Bio::Fasta::Report::Hit::Query)
entry_id (Bio::Lasergene)
entry_id (Bio::DB)
entry_id (Bio::KEGG::COMPOUND)
entry_id (Bio::TargetP::Report)
entry_id (Bio::KEGG::REACTION)
entry_id (Bio::FANTOM::MaXML::Annotation)
entry_id (Bio::SQL::Sequence)
entry_id (Bio::EMBL)
entry_id (Bio::Fastq)
entry_id (Bio::KEGG::DRUG)
entry_id (Bio::FANTOM::MaXML)
entry_id (Bio::FastaFormat)
entry_id (Bio::GenBank)
entry_id (Bio::KEGG::ORTHOLOGY)
entry_id (Bio::TRANSFAC)
entry_id (Bio::KEGG::GENES)
entry_id (Bio::KEGG::GLYCAN)
entry_id (Bio::AAindex)
entry_id (Bio::PDB)
entry_id (Bio::SPTR)
entry_id= (Bio::SQL::Sequence)
entry_name (Bio::EMBL)
entry_name (Bio::SPTR)
entry_pos_flag (Bio::FlatFile)
entry_pos_flag= (Bio::FlatFile)
entry_raw (Bio::FlatFile)
entry_start_pos (Bio::Blast::Report::BlastXmlSplitter)
entry_start_pos (Bio::FlatFile)
entry_version (Bio::EMBL)
enzyme_name? (Bio::REBASE)
enzyme_name? (Bio::RestrictionEnzyme)
enzymes (Bio::KEGG::COMPOUND)
enzymes (Bio::KEGG::REACTION)
enzymes (Bio::REBASE)
enzymes (Bio::KEGG::GLYCAN)
eof? (Bio::FlatFile::BufferedInputStream)
eof? (Bio::FlatFile)
equals? (Bio::Locations)
equation (Bio::KEGG::REACTION)
error_msg (Bio::SOFT)
error_probabilities (Bio::Fastq)
errorlog (Bio::ClustalW)
escape_shell (Bio::Command)
escape_shell_unix (Bio::Command)
escape_shell_windows (Bio::Command)
escaped_cut_symbol (Bio::RestrictionEnzyme::CutSymbol::CutSymbol__)
escaped_cut_symbol (Bio::RestrictionEnzyme::CutSymbol)
esearch (Bio::NCBI::REST)
esearch (Bio::PubMed)
esearch (Bio::PubMed)
esearch (Bio::NCBI::REST)
esearch_count (Bio::NCBI::REST)
esearch_count (Bio::NCBI::REST)
est (Bio::NCBI::REST::ESearch::Methods)
establish_connection (Bio::SQL)
evaluate (BiorubyController)
evalue (Bio::Blast::Report::Hit)
evalue (Bio::Blast::Default::Report::Hit)
evalue (Bio::Iprscan::Report::Match)
evalue (Bio::Fasta::Report::Hit)
events (Bio::Tree::Node)
evidence (Bio::FANTOM::MaXML::Annotations)
exec (Bio::PSORT::CGIDriver)
exec (Bio::EMBOSS)
exec (Bio::PSORT::PSORT1)
exec (Bio::PSORT::PSORT2)
exec (Bio::PTS1)
exec (Bio::Sim4)
exec_ddbj (Bio::Blast::Remote::DDBJ)
exec_local (Bio::Sim4)
exists? (Bio::DB)
exists_accession (Bio::SQL)
exists_database (Bio::SQL)
exit_code (Bio::Blast::WU::Report)
exit_code_message (Bio::Blast::WU::Report)
exon_type_long (Bio::Genscan::Report::Exon)
exons (Bio::Spidey::Report::Hit)
exons (Bio::Sim4::Report::Hit)
exons (Bio::Blat::Report::Hit)
expect (Bio::Blast::WU::Report)
expect (Bio::Blast::Report)
expected (Bio::ContingencyTable)
export_tsv (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
exportview (Bio::Ensembl::Base)
exportview (Bio::Ensembl)
external_merge_proc (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
external_merge_sort_proc (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
external_sort_proc (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
extract_biosequence (Bio::PhyloXML::Node)
extract_key (Bio::Alignment::OriginalPrivate)
extract_seq (Bio::Alignment::OriginalPrivate)
fa (Bio::TRANSFAC::FACTOR)
false_neg (Bio::PROSITE)
false_negative_hits (Bio::PROSITE)
false_pos (Bio::PROSITE)
false_positive_hits (Bio::PROSITE)
false_positive_sequences (Bio::PROSITE)
fasta (Bio::FastaFormat)
fatal_errors (Bio::Blast::WU::Report)
feature= (Bio::SQL::Sequence)
features (Bio::EMBL)
features (Bio::NCBIDB::Common)
features (Bio::DAS)
features (Bio::SQL::Sequence)
fetch (Bio::Fetch)
fetch (Bio::DB)
fetch (Bio::Blast::Fastacmd)
fetch_accession (Bio::SQL)
fetch_id (Bio::SQL)
ff (Bio::TRANSFAC::FACTOR)
fftns (Bio::MAFFT)
fftnsi (Bio::MAFFT)
fh (Bio::EMBL)
field (Bio::LITDB)
fileids (Bio::FlatFileIndex::DataBank)
filename (Bio::FlatFileIndex::BDB_1::PrimaryNameSpace)
filename (Bio::FlatFileIndex::Flat_1::SecondaryNameSpace)
filename (Bio::FlatFileIndex::BDB_1::SecondaryNameSpace)
filename (Bio::FlatFileIndex::BDBwrapper)
filename (Bio::FlatFileIndex::DataBank)
filename (Bio::FlatFileIndex::Template::NameSpace)
filename (Bio::FlatFileIndex::Flat_1::PrimaryNameSpace)
filenames (Bio::FlatFileIndex::FileIDs)
fill (String)
filter (Bio::Blast::Report)
find_atom (Bio::PDB::AtomFinder)
find_chain (Bio::PDB::ChainFinder)
find_flat_dir (Bio::Shell::Ghost)
find_hetatm (Bio::PDB::HetatmFinder)
find_heterogen (Bio::PDB::HeterogenFinder)
find_match_locations (Bio::RestrictionEnzyme::Analysis)
find_model (Bio::PDB::ModelFinder)
find_residue (Bio::PDB::ResidueFinder)
finder (Bio::PDB::Utils)
first (Bio::Features)
first (Bio::Locations)
flag_append (Bio::FlatFileIndex::BDBdefault)
flag_read (Bio::FlatFileIndex::BDBdefault)
flag_write (Bio::FlatFileIndex::BDBdefault)
fold (String)
for_display (Bio::RestrictionEnzyme::Range::SequenceRange::Fragment)
for_display (Bio::RestrictionEnzyme::Range::SequenceRange::Fragments)
for_io (Bio::PhyloXML::Parser)
for_io (Bio::FlatFile::BufferedInputStream)
foreach (Bio::FlatFile)
format (Bio::Fastq)
format (Bio::Reference)
format (Bio::FlatFileIndex::DataBank)
format= (Bio::Fastq)
format= (Bio::Fasta)
format= (Bio::FlatFileIndex::DataBank)
format_raw (Bio::Iprscan::Report)
formats (Bio::Fetch)
formatstring2class (Bio::FlatFileIndex)
formul (Bio::PDB::ChemicalComponent)
formula (Bio::KEGG::COMPOUND)
formula (Bio::KEGG::DRUG)
forward_complement (Bio::Sequence::NA)
forward_complement! (Bio::Sequence::NA)
found_again? (Bio::Blast::Default::Report::Hit)
fragments (Bio::RestrictionEnzyme::Range::SequenceRange)
fragments_for_display (Bio::RestrictionEnzyme::Analysis)
from= (Bio::PhyloXML::ProteinDomain)
ft (Bio::EMBL)
ft (Bio::SPTR)
ft (Bio::TRANSFAC::FACTOR)
function (Bio::PTS1)
gained_count= (Bio::PhyloXML::BinaryCharacters)
gap_char (Bio::Alignment::PropertyMethods)
gap_extend (Bio::Blast::Report)
gap_length_weight (Bio::GCG::Msf)
gap_open (Bio::Blast::Report)
gap_regexp (Bio::Alignment::PropertyMethods)
gap_weight (Bio::GCG::Msf)
gapped_entropy (Bio::Blast::Default::Report)
gapped_kappa (Bio::Blast::Default::Report)
gapped_lambda (Bio::Blast::Default::Report)
gapped_pos (Bio::Alignment::GAP)
gbposition (Bio::KEGG::GENES)
gc_content (Bio::Sequence::NA)
gc_percent (Bio::Sequence::NA)
gc_skew (Bio::Sequence::NA)
gene (Bio::KEGG::GENES)
gene_name (Bio::SPTR)
gene_name (Bio::FANTOM::MaXML::Annotations)
gene_names (Bio::SPTR)
general (Bio::Reference)
generate (Bio::Phylip::DistanceMatrix)
generate_colored_text (Bio::Shell::ColoredCodonTable)
generate_mono_text (Bio::Shell::ColoredCodonTable)
generate_xml (Bio::PhyloXML::Writer)
genes (Bio::KEGG::ORTHOLOGY)
genes (Bio::KEGG::ENZYME)
genes (Bio::KEGG::GENES)
genes_as_hash (Bio::KEGG::ORTHOLOGY)
genes_as_hash (Bio::KEGG::Common::GenesAsHash)
genes_as_hash (Bio::KEGG::ENZYME)
genes_as_strings (Bio::KEGG::ENZYME)
genes_as_strings (Bio::KEGG::ORTHOLOGY)
genome_biol (Bio::Reference)
genome_res (Bio::Reference)
genomenet (Bio::Blast::Remote)
genomic (Bio::Spidey::Report::Hit)
geometricCentre (Bio::PDB::Utils)
get (Bio::FANTOM::MaXML::Sequences)
get (Bio::Blast::NCBIOptions)
get (Bio::FlatFileIndex::FileID)
get (Bio::DB)
get (Bio::FastaDefline)
getAsyncResult (Bio::DDBJ::XML::RequestManager::REST)
get_aaseqs (Bio::KEGG::API)
get_all_best_best_neighbors_by_gene (Bio::KEGG::API)
get_all_best_neighbors_by_gene (Bio::KEGG::API)
get_all_by_qualifier (Bio::FANTOM::MaXML::Annotations)
get_all_by_type (Bio::FastaDefline)
get_all_genes_by_motifs (Bio::KEGG::API)
get_all_genes_by_organism (Bio::KEGG::API)
get_all_linkdb_by_entry (Bio::KEGG::API)
get_all_oc_members_by_gene (Bio::KEGG::API)
get_all_paralogs_by_gene (Bio::KEGG::API)
get_all_pc_members_by_gene (Bio::KEGG::API)
get_all_property (Bio::Alignment::PropertyMethods)
get_all_reverse_best_neighbors_by_gene (Bio::KEGG::API)
get_attribute (Bio::GFF::GFF2::Record)
get_attributes (Bio::GFF::GFF2::Record)
get_blocks (Bio::Nexus)
get_blocks_by_name (Bio::Nexus)
get_by_id (Bio::FlatFileIndex)
get_by_id (Bio::Blast::Fastacmd)
get_by_id (Bio::FANTOM)
get_by_id (Bio::Fetch)
get_by_qualifier (Bio::FANTOM::MaXML::Annotations)
get_by_type (Bio::FastaDefline)
get_characters_blocks (Bio::Nexus)
get_characters_string (Bio::Nexus::CharactersBlock)
get_characters_strings_by_name (Bio::Nexus::CharactersBlock)
get_data_blocks (Bio::Nexus)
get_database (Bio::Registry)
get_datatype (Bio::Nexus::CharactersBlock)
get_definitions (Bio::KEGG::API)
get_distances_blocks (Bio::Nexus)
get_dna (Bio::DAS)
get_dsn (Bio::DAS)
get_edge (Bio::Tree)
get_edge_distance (Bio::Tree)
get_edge_distance_string (Bio::Tree)
get_edge_merged (Bio::Tree)
get_entries (Bio::KEGG::API)
get_entry (Bio::Blast::Report::BlastXmlSplitter)
get_entry (Bio::Blast::RPSBlast::RPSBlastSplitter)
get_entry (Bio::FlatFile::Splitter::Template)
get_entry (Bio::FlatFile::Splitter::LineOriented)
get_entry (Bio::Fasta::Report::FastaFormat10Splitter)
get_entry (Bio::FlatFile::Splitter::Default)
get_entry_points (Bio::DAS)
get_features (Bio::DAS)
get_flatfile_data (Bio::FlatFileIndex::DataBank)
get_gap_character (Bio::Nexus::CharactersBlock)
get_heterogen_by_id (Bio::PDB::Chain)
get_match_character (Bio::Nexus::CharactersBlock)
get_matrix (Bio::Nexus::CharactersBlock)
get_matrix (Bio::Nexus::DistancesBlock)
get_max_col (Bio::Nexus::NexusMatrix)
get_max_row (Bio::Nexus::NexusMatrix)
get_missing (Bio::Nexus::CharactersBlock)
get_name (Bio::Nexus::GenericBlock)
get_name (Bio::Nexus::NexusMatrix)
get_naseqs (Bio::KEGG::API)
get_node_bootstrap (Bio::Tree)
get_node_bootstrap_string (Bio::Tree)
get_node_by_name (Bio::Tree)
get_node_name (Bio::Tree)
get_number_of_characters (Bio::Nexus::CharactersBlock)
get_number_of_characters (Bio::Nexus::DistancesBlock)
get_number_of_taxa (Bio::Nexus::CharactersBlock)
get_number_of_taxa (Bio::Nexus::DistancesBlock)
get_number_of_taxa (Bio::Nexus::TaxaBlock)
get_parsed_entry (Bio::FlatFile::Splitter::Template)
get_parsed_entry (Bio::FlatFile::Splitter::LineOriented)
get_parsed_entry (Bio::Blast::Report::BlastXmlSplitter)
get_record (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
get_record_class (Bio::PDB::Record)
get_record_class (Bio::PDB::ChemicalComponent::Record)
get_residue_by_id (Bio::PDB::Chain)
get_residue_id_from_atom (Bio::PDB::Residue)
get_row_name (Bio::Nexus::CharactersBlock)
get_row_string (Bio::Nexus::NexusMatrix)
get_row_strings_by_name (Bio::Nexus::NexusMatrix)
get_seqfeature (Bio::SQL::Sequence)
get_sequence (Bio::Nexus::CharactersBlock)
get_sequence (Bio::DAS)
get_sequences_by_name (Bio::Nexus::CharactersBlock)
get_taxa (Bio::Nexus::DataBlock)
get_taxa (Bio::Nexus::TaxaBlock)
get_taxa_blocks (Bio::Nexus)
get_tokens (Bio::Nexus::GenericBlock)
get_tree (Bio::Nexus::TreesBlock)
get_tree_names (Bio::Nexus::TreesBlock)
get_tree_strings (Bio::Nexus::TreesBlock)
get_tree_strings_by_name (Bio::Nexus::TreesBlock)
get_trees_blocks (Bio::Nexus)
get_trees_by_name (Bio::Nexus::TreesBlock)
get_triangle (Bio::Nexus::DistancesBlock)
get_types (Bio::DAS)
get_value (Bio::Nexus::NexusMatrix)
getc (Bio::FlatFile::BufferedInputStream)
getoptlong (Bio::Shell::Setup)
gets (Bio::FlatFile)
gets (Bio::FlatFile::BufferedInputStream)
gi (Bio::FastaDefline)
gi (Bio::NCBIDB::Common)
gi (Bio::FastaFormat)
glycans (Bio::KEGG::COMPOUND)
gn (Bio::SPTR)
go_ids (Bio::GO::External2go)
go_terms (Bio::Iprscan::Report::Match)
go_terms (Bio::GO::External2go)
goid (Bio::GO::GeneAssociation)
goid2term (Bio::GO::Ontology)
green= (Bio::PhyloXML::BranchColor)
gss (Bio::NCBI::REST::ESearch::Methods)
gsub_entities (Bio::FANTOM::MaXML)
guess (Bio::Sequence)
guess (Bio::FlatFile::AutoDetect::RuleDebug)
guess (Bio::FlatFile::AutoDetect::RuleProc)
guess (Bio::FlatFile::AutoDetect::RuleTemplate)
guess (Bio::FlatFile::AutoDetect::RuleRegexp2)
guess (Bio::Sequence)
guess (Bio::FlatFile::AutoDetect::RuleRegexp)
has_gap? (Bio::Alignment::SiteMethods)
has_key? (Bio::Alignment::OriginalAlignment)
have_results (BiorubyHelper)
header (Bio::ClustalW::Report)
header (Bio::Sequence::NA::MidiTrack)
helix (Bio::TMHMM::Report)
helix (Bio::PDB)
helper_for_to_array_index (Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation)
hetatm (Bio::PDB::Heterogen)
hetatm (Bio::PDB::Residue)
hetatms (Bio::PDB::HetatmFinder)
heterogens (Bio::PDB::HeterogenFinder)
hetnam (Bio::PDB::ChemicalComponent)
hetsyn (Bio::PDB::ChemicalComponent)
hi (Bio::SPTR)
higet_in_fasta (Bio::HGC::HiGet)
higet_in_xml (Bio::HGC::HiGet)
higher_priority_elements (Bio::FlatFile::AutoDetect::RuleSpecial)
history (BiorubyController)
history_file (Bio::Shell::Core)
hit2acc (Bio::Hinv)
hit_cnt (Bio::Hinv)
hit_definition (Bio::Hinv)
hit_from (Bio::Spidey::Report::SegmentPair)
hit_from (Bio::Sim4::Report::SegmentPair)
hit_id (Bio::Spidey::Report::Hit)
hit_id (Bio::Sim4::Report::Hit)
hit_pubmedid (Bio::Hinv)
hit_strand (Bio::Spidey::Report::SegmentPair)
hit_to (Bio::Spidey::Report::SegmentPair)
hit_to (Bio::Sim4::Report::SegmentPair)
hit_xml (Bio::Hinv)
hits (Bio::Blast::Report)
hits (Bio::Blast::Bl2seq::Report::Iteration)
hits (Bio::Blast::Default::Report)
hits (Bio::Blast::Default::Report::Iteration)
hits_for_pattern (Bio::Blast::Default::Report::Iteration)
hits_found_again (Bio::Blast::Default::Report::Iteration)
hits_newly_found (Bio::Blast::Default::Report::Iteration)
hix2hit (Bio::Hinv)
hix_cnt (Bio::Hinv)
hix_represent (Bio::Hinv)
ho (Bio::TRANSFAC::FACTOR)
hseq (Bio::Spidey::Report::SegmentPair)
hseq (Bio::Sim4::Report::SegmentPair)
hsp_len (Bio::Blast::Report)
hsps (Bio::Spidey::Report::Hit)
hsps (Bio::Blat::Report::Hit)
hsps (Bio::Sim4::Report::Hit)
http_post_form (Bio::Command)
human (Bio::Ensembl)
iCode= (Bio::PDB::Residue)
icode (Bio::Sequence::NA::MidiTrack)
id (Bio::GFF::GFF3::Record)
id= (Bio::GFF::GFF3::Record)
id_line (Bio::SPTR)
id_line (Bio::EMBL)
id_search (Bio::Hinv)
id_strings (Bio::FastaDefline)
id_strings (Bio::FANTOM::MaXML::Sequence)
id_strings (Bio::FANTOM::MaXML::Sequences)
identifier (Bio::SQL::Sequence)
identifier= (Bio::SQL::Sequence)
identifiers (Bio::FastaFormat)
identity (Bio::Blast::Report::Hit)
identity (Bio::Blast::Default::Report::Hit)
identity (Bio::Fasta::Report::Hit)
illegal_bases (Bio::Sequence::NA)
import_tsv_files (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
imsut (Bio::PSORT::PSORT1)
imsut (Bio::PSORT::PSORT2)
in (Bio::TRANSFAC::FACTOR)
include? (Bio::FlatFileIndex)
include? (Bio::RestrictionEnzyme::Range::HorizontalCutRange)
include? (Bio::RestrictionEnzyme::Range::CutRanges)
include? (Bio::FlatFileIndex::Template::NameSpace)
include? (Bio::RestrictionEnzyme::Range::VerticalCutRange)
include? (Bio::Tree)
include_in_namespaces? (Bio::FlatFileIndex)
include_in_primary? (Bio::FlatFileIndex)
inclusion (Bio::Blast::Report)
index (BiorubyController)
index (Bio::Alignment::OriginalAlignment)
index (Bio::AAindex1)
index_type= (Bio::FlatFileIndex::DataBank)
inhibitors (Bio::KEGG::ENZYME)
init (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
init_fileids (Bio::FlatFileIndex::DataBank)
init_with_array (Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair)
init_with_sorted_tsv_file (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
initialize_from_string (Bio::PDB::Record)
initialize_with_pattern_and_cut_locations (Bio::RestrictionEnzyme::DoubleStranded)
initialize_with_pattern_and_cut_symbols (Bio::RestrictionEnzyme::DoubleStranded)
initialize_with_rebase (Bio::RestrictionEnzyme::DoubleStranded)
initiation_score (Bio::Genscan::Report::Exon)
input (Bio::Sequence)
insert_node (Bio::Tree)
inspect (Bio::PDB::Chain)
inspect (Bio::FlatFile::AutoDetect::RulesArray)
inspect (Bio::PDB::Record)
inspect (Bio::PDB::Residue)
inspect (Bio::PDB)
inspect (Bio::Tree::Node)
inspect (Bio::PDB::Model)
inspect (Bio::FlatFile::AutoDetect)
inspect (Bio::Tree::Edge)
install_savedir (Bio::Shell::Setup)
interleaved? (Bio::Phylip::PhylipFormat)
internal_http (Bio::TogoWS::REST)
internal_sort_proc (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
introns (Bio::Sim4::Report::Hit)
introns (Bio::Spidey::Report::Hit)
io (Bio::FlatFile)
ip (Bio::MEDLINE)
ipr_id (Bio::Iprscan::Report::Match)
ipr_odescription (Bio::Iprscan::Report::Match)
is_aligned= (Bio::PhyloXML::Sequence)
is_aligned? (Bio::PhyloXML::Sequence)
is_empty? (Bio::Nexus::NexusMatrix)
is_gap? (Bio::Alignment::PropertyMethods)
is_prior_to (Bio::FlatFile::AutoDetect::RuleTemplate)
isolate (Bio::Alignment::OriginalAlignment)
issue (Bio::MEDLINE)
iubmb_reactions (Bio::KEGG::ENZYME)
journal (Bio::NCBI::REST::EFetch::Methods)
journal (Bio::MEDLINE)
journal (Bio::AAindex)
journal (Bio::LITDB)
journal (Bio::NCBI::REST::ESearch::Methods)
jrnl (Bio::PDB)
kappa (Bio::Blast::Default::Report)
kappa (Bio::Blast::Report)
kcf (Bio::KEGG::COMPOUND)
kcf (Bio::KEGG::DRUG)
kcf (Bio::KEGG::GLYCAN)
kegg_reactions (Bio::KEGG::ENZYME)
keggapi_definition2tab (Bio::Shell::Private)
keggclass (Bio::KEGG::ORTHOLOGY)
keggclass (Bio::KEGG::GLYCAN)
keggclasses (Bio::KEGG::ORTHOLOGY)
keggorg2taxo (Bio::KEGG::Keggtab)
keggorg2taxonomy (Bio::KEGG::Keggtab)
keys (Bio::FlatFileIndex::FileIDs)
keys (Bio::FlatFileIndex::BDBwrapper)
keyword (Bio::LITDB)
keyword_search (Bio::Hinv)
keywords (Bio::EMBLDB::Common)
keywords (Bio::NCBIDB::Common)
keywords (Bio::PDB)
korg2taxo (Bio::KEGG::Keggtab)
korg2taxonomy (Bio::KEGG::Keggtab)
kw (Bio::EMBLDB::Common)
lambda (Bio::Blast::Report)
lambda (Bio::Blast::Default::Report)
lap_at (Bio::Fasta::Report::Hit)
lap_at (Bio::Blast::Report::Hit)
lap_at (Bio::Blast::Default::Report::Hit)
lap_over (Bio::Fasta::Report)
larger_than_zero (Bio::Nexus::Util)
last (Bio::Locations)
last (Bio::Features)
lat= (Bio::PhyloXML::Point)
leaves (Bio::Tree)
left_padding (Bio::RestrictionEnzyme::StringFormatting)
len (Bio::Blast::Default::Report::Hit)
len (Bio::Blat::Report::Hit)
len (Bio::Spidey::Report::Hit)
len (Bio::Sim4::Report::Hit)
length (Bio::Fasta::Report::Hit::Query)
length (Bio::GenBank)
length (Bio::NBRF)
length (Bio::FastaNumericFormat)
length (Bio::Locations)
length (Bio::Iprscan::Report::Match)
length (Bio::GenPept)
length (Bio::KEGG::GENOME)
length (Bio::SQL::Sequence)
length (Bio::TargetP::Report)
length (Bio::FastaFormat)
length (Bio::Meme::Motif)
length= (Bio::PhyloXML::DomainArchitecture)
length= (Bio::SQL::Sequence)
library_id (Bio::FANTOM::MaXML::Sequence)
lineage (Bio::KEGG::GENOME)
list_classes (BiorubyController)
list_databases (Bio::SQL)
list_entries (Bio::SQL)
list_falsenegative (Bio::PROSITE)
list_falsepositive (Bio::PROSITE)
list_methods (BiorubyController)
list_methods (Bio::SOAPWSDL)
list_modules (BiorubyController)
list_output_formats (Bio::Sequence::Format)
list_potentialhit (Bio::PROSITE)
list_sequences (Bio::DAS)
list_truepositive (Bio::PROSITE)
list_unknown (Bio::PROSITE)
list_xref (Bio::PROSITE)
load_config (Bio::Shell::Ghost)
load_config_file (Bio::Shell::Ghost)
load_history (Bio::Shell::Ghost)
load_history_file (Bio::Shell::Ghost)
load_object (Bio::Shell::Ghost)
load_object_file (Bio::Shell::Ghost)
load_parameters (Bio::PAML::Common)
load_plugin (Bio::Shell::Ghost)
load_plugin_dir (Bio::Shell::Ghost)
load_session (Bio::Shell::Ghost)
load_yaml (Bio::REBASE)
loc (Bio::TargetP::Report)
local (Bio::Fasta)
local (Bio::Blast)
local_variables (BiorubyHelper)
locations (Bio::KEGG::GENES)
locations (Bio::Feature)
locus (Bio::GenPept)
locus (Bio::GenBank)
locus (Bio::FastaDefline)
locus (Bio::FastaFormat)
locus (Bio::NCBIDB::Common)
log (Bio::Sim4)
log (Bio::MAFFT)
log (Bio::ClustalW)
log= (Bio::SOAPWSDL)
logy_minus_logx (Bio::KEGG::EXPRESSION)
long= (Bio::PhyloXML::Point)
longer_than_zero (Bio::Nexus::Util)
losses= (Bio::PhyloXML::Events)
lost_count= (Bio::PhyloXML::BinaryCharacters)
lower_priority_elements (Bio::FlatFile::AutoDetect::RuleSpecial)
lowest_common_ancestor (Bio::Tree)
lstrip (Bio::Alignment::OriginalAlignment)
lstrip! (Bio::Alignment::EnumerableExtension)
ma (Bio::PROSITE)
ma (Bio::TRANSFAC::MATRIX)
ma2re (Bio::PROSITE)
make_cgi_params (Bio::Command)
make_cgi_params_key_value (Bio::Command)
make_command_line (Bio::Command)
make_command_line_options (Bio::Blast::NCBIOptions)
make_command_line_unix (Bio::Command)
make_command_line_windows (Bio::Command)
make_default (Bio::FlatFile::AutoDetect)
makeindex (Bio::FlatFileIndex)
makeindexBDB (Bio::FlatFileIndex::Indexer)
makeindexFlat (Bio::FlatFileIndex::Indexer)
manifest (BiorubyGenerator)
mapped_to? (Bio::Map::ActsLikeMarker)
mapping (Bio::FlatFileIndex::BDB_1::SecondaryNameSpace)
mapping (Bio::FlatFileIndex::Flat_1::PrimaryNameSpace)
mapping (Bio::FlatFileIndex::BDB_1::PrimaryNameSpace)
mapping (Bio::FlatFileIndex::Template::NameSpace)
mapping (Bio::FlatFileIndex::Flat_1::SecondaryNameSpace)
mappings_on (Bio::Map::ActsLikeMarker)
mass (Bio::KEGG::COMPOUND)
mass (Bio::KEGG::GLYCAN)
mass (Bio::KEGG::DRUG)
match (Bio::Blat::Report::Hit)
match_end (Bio::Iprscan::Report::Match)
match_line (Bio::Alignment::EnumerableExtension)
match_line (Bio::ClustalW::Report)
match_line_amino (Bio::Alignment::EnumerableExtension)
match_line_amino (Bio::Alignment::SiteMethods)
match_line_nuc (Bio::Alignment::EnumerableExtension)
match_line_nuc (Bio::Alignment::SiteMethods)
match_start (Bio::Iprscan::Report::Match)
matrix (Bio::AAindex2)
matrix (Bio::Blast::Report)
max (Bio::RestrictionEnzyme::Range::CutRanges)
max_repeat (Bio::PROSITE)
max_vertical (Bio::RestrictionEnzyme::Range::CutRanges)
maxids (Bio::Fetch)
maximum= (Bio::PhyloXML::Date)
merge (Bio::Alignment::OriginalAlignment)
merge! (Bio::Alignment::OriginalAlignment)
mesh (Bio::MEDLINE)
message (Bio::Blast::Default::Report)
message (Bio::Blast::Report)
method_missing (Bio)
method_missing (Bio::NCBI::REST::ESearch::Methods)
method_missing (Bio::Iprscan::Report::Match)
method_missing (Bio::Registry::DB)
method_missing (Bio::FastaDefline)
method_missing (Bio::KEGG::API)
method_missing (Bio::NCBI::SOAP)
method_name (Bio::Iprscan::Report::Match)
mh (Bio::MEDLINE)
midline (Bio::Blast::Default::Report::Hit)
midline (Bio::Blast::Report::Hit)
milli_bad (Bio::Blat::Report::Hit)
min (Bio::RestrictionEnzyme::Range::CutRanges)
min_vertical (Bio::RestrictionEnzyme::Range::CutRanges)
minimum= (Bio::PhyloXML::Date)
mismatch (Bio::Blat::Report::Hit)
missing_char (Bio::Alignment::PropertyMethods)
missing_mrna_ends (Bio::Spidey::Report::Hit)
mito (Bio::Shell::Demo)
mktmpdir (Bio::Command)
mm (Bio::TRANSFAC::SITE)
mol_seq= (Bio::PhyloXML::Sequence)
molecular_weight (Bio::Sequence::NA)
molecular_weight (Bio::Sequence::AA)
molecule (Bio::EMBL)
molecule (Bio::SPTR)
molecule_type (Bio::SPTR)
molecule_type (Bio::EMBL)
moltype (Bio::Fasta::Report::Hit::Query)
motif (Bio::KEGG::GENES)
motifs (Bio::KEGG::ENZYME)
mouse (Bio::Ensembl)
mrna (Bio::Spidey::Report)
mrna (Bio::Spidey::Report::Hit)
mx (Bio::TRANSFAC::FACTOR)
n_s (Bio::Blat::Report::Hit)
na (Bio::TRANSFAC::MATRIX)
na (Bio::Sequence)
na (Bio::NucleicAcid::Data)
nalen (Bio::KEGG::GENES)
nalen (Bio::Fastq)
nalen (Bio::NBRF)
nalen (Bio::FastaFormat)
nalen (Bio::KEGG::GENOME)
nalen (Bio::GenBank)
name (Bio::PROSITE)
name (Bio::KEGG::REACTION)
name (Bio::NucleicAcid::Data)
name (Bio::AminoAcid::Data)
name (Bio::KEGG::GLYCAN)
name (Bio::KEGG::Keggtab)
name (Bio::KEGG::COMPOUND)
name (Bio::KEGG::ORTHOLOGY)
name (Bio::KEGG::GENES)
name (Bio::SQL::Sequence)
name (Bio::KEGG::DRUG)
name (Bio::KEGG::GENOME)
name (Bio::KEGG::ENZYME)
name (Bio::TargetP::Report)
name2one (Bio::AminoAcid::Data)
name2three (Bio::AminoAcid::Data)
name= (Bio::FlatFile::AutoDetect::RuleSpecial)
name= (Bio::SQL::Sequence)
name_by_abbrev (Bio::KEGG::Keggtab)
names (Bio::KEGG::ORTHOLOGY)
names (Bio::KEGG::ENZYME)
names (Bio::Sequence::AA)
names (Bio::FlatFileIndex::Indexer::NameSpaces)
names (Bio::KEGG::COMPOUND)
names (Bio::KEGG::KGML::Entry)
names (Bio::KEGG::DRUG)
names (Bio::FlatFileIndex::NameSpaces)
names (Bio::NucleicAcid::Data)
names (Bio::AminoAcid::Data)
names (Bio::Sequence::NA)
namespaces (Bio::FlatFileIndex)
nar (Bio::Reference)
naseq (Bio::NBRF)
naseq (Bio::Fastq)
naseq (Bio::DBGET)
naseq (Bio::GenBank)
naseq (Bio::KEGG::GENES)
naseq (Bio::GCG::Seq)
naseq (Bio::EMBL)
naseq (Bio::FastaFormat)
nature (Bio::Reference)
natype (Bio::GenBank)
new (Bio::GCG::Seq)
new (Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts)
new (Bio::Fetch)
new (Bio::Blast::RPSBlast::Report)
new (Bio::Hinv::HitDefinition)
new (Bio::Hinv::HixRepresent)
new (Bio::Blast::RPSBlast::Report::Iteration)
new (Bio::Blast::RPSBlast::RPSBlastSplitter)
new (Bio::Sequence::NA)
new (Bio::Hinv::KeywordSearch)
new (Bio::Sequence::Format::Formatter::Fastq)
new (Bio::Hinv::HitPubmedId)
new (Bio::Hinv::HixCnt)
new (Bio::Sequence::Format::Formatter::Fasta_numeric)
new (Bio::Hinv::IdSearch)
new (Bio::KEGG::Keggtab)
new (Bio::Hinv::HitXML)
new (Bio::Sequence::AA)
new (Bio::Sequence::Format::FormatterBase)
new (Bio::Sequence::Format::Formatter::Fasta)
new (Bio::Features)
new (Bio::Features)
new (Bio::Blast::WU::Report::Hit)
new (Bio::Hinv::Hit2acc)
new (Bio::Blast::WU::Report::Iteration)
new (Bio::Hinv::Hix2hit)
new (Bio::TargetP::Report)
new (Bio::RestrictionEnzyme::Range::SequenceRange)
new (Bio::KEGG::KGML)
new (Bio::Hinv::HitCnt)
new (Bio::Alignment::FactoryTemplate::Simple)
new (Bio::Shell::Setup)
new (Bio::FastaDefline)
new (Bio::Blast::Remote::DDBJ)
new (Bio::AAindex)
new (Bio::Blast::Remote::GenomeNet)
new (Bio::FlatFileIndex::BDBwrapper)
new (Bio::RestrictionEnzyme::Range::VerticalCutRange)
new (Bio::RestrictionEnzyme::Range::HorizontalCutRange)
new (Bio::Blast::Report)
new (Bio::KEGG::Keggtab::DB)
new (Bio::Newick)
new (Bio::Blat::Report)
new (Bio::Alignment::MultiFastaFormat)
new (Bio::GO::Ontology)
new (Bio::EMBLDB)
new (Bio::Alignment::OriginalAlignment)
new (Bio::EMBLDB::Common)
new (Bio::GO::GeneAssociation)
new (Bio::Sequence)
new (Bio::FlatFileIndex::FileIDs)
new (Bio::GO::External2go)
new (Bio::Shell::Web::Results)
new (Bio::PDB)
new (Bio::Alignment::OriginalAlignment)
new (Bio::Shell::Web)
new (Bio::Blat::Report::SegmentPair)
new (Bio::ContingencyTable)
new (Bio::Blat::Report::SeqDesc)
new (Bio::Blat::Report::Hit)
new (Bio::Nexus::DistancesBlock)
new (Bio::Nexus::DataBlock)
new (Bio::Nexus::GenericBlock)
new (Bio::Blast::Report::Hsp)
new (Bio::Blast::Report::BlastXmlSplitter)
new (Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation)
new (Bio::Nexus::TreesBlock)
new (Bio::LITDB)
new (Bio::Nexus::CharactersBlock)
new (Bio::Registry)
new (Bio::Nexus::NexusMatrix)
new (Bio::Registry::DB)
new (Bio::Blast::Report::Hit)
new (Bio::Nexus::TaxaBlock)
new (Bio::Nexus)
new (Bio::SOSUI::Report)
new (Bio::Fastq::Error)
new (Bio::Shell::Demo)
new (Bio::Blast::Default::Report::Iteration)
new (Bio::REBASE)
new (Bio::Pathway)
new (Bio::Fastq::FormatData)
new (Bio::DAS)
new (Bio::Sequence::Format::Formatter::Qual)
new (Bio::Sequence::DBLink)
new (Bio::Fastq)
new (Bio::Map::SimpleMap)
new (Bio::Blast::Report::Iteration)
new (Bio::Map::Mapping)
new (Bio::Blast::Fastacmd)
new (Bio::Map::Marker)
new (Bio::PAML::Common)
new (Bio::Shell::ColoredCodonTable)
new (Bio::HMMER::Report::Hit)
new (Bio::Blast::Bl2seq::Report::Iteration)
new (Bio::Iprscan::Report::Match)
new (Bio::Blast::NCBIOptions)
new (Bio::KEGG::GLYCAN)
new (Bio::GFF)
new (Bio::Shell::Irb)
new (Bio::HMMER::Report::Hsp)
new (Bio::Shell::Script)
new (Bio::Iprscan::Report)
new (Bio::FlatFileIndex::DataBank)
new (Bio::HMMER::Report)
new (Bio::KEGG::GENES)
new (Bio::DAS::FEATURE)
new (Bio::RestrictionEnzyme::SingleStrand)
new (Bio::EMBOSS)
new (Bio::Locations)
new (Bio::GFF::GFF2)
new (Bio::Spidey::Report)
new (Bio::HMMER)
new (Bio::GFF::GFF2::Record)
new (Bio::Scf)
new (Bio::PAML::Common::Report)
new (Bio::TogoWS::REST)
new (Bio::DAS::GROUP)
new (Bio::PAML::Codeml::Report)
new (Bio::Spidey::Report::SegmentPair)
new (Bio::KEGG::Taxonomy)
new (Bio::TRANSFAC::GENE)
new (Bio::PAML::Codeml::Rates)
new (Bio::Reference)
new (Bio::GenBank::Locus)
new (Bio::Phylip::PhylipFormat)
new (Bio::Phylip::DistanceMatrix)
new (Bio::FlatFileIndex::NameSpaces)
new (Bio::PDB::DataType::Pdb_LString)
new (Bio::TRANSFAC::SITE)
new (Bio::Spidey::Report::SeqDesc)
new (Bio::PDB::DataType::Pdb_Specification_list)
new (Bio::Spidey::Report::Hit)
new (Bio::PhyloXML::Parser)
new (Bio::PDB::DataType::Pdb_StringRJ)
new (Bio::AAindex1)
new (Bio::DAS::ENTRY_POINT)
new (Bio::Hinv::Acc2hit)
new (Bio::Tree)
new (Bio::TRANSFAC::FACTOR)
new (Bio::TRANSFAC::CELL)
new (Bio::PhyloXML::Confidence)
new (Bio::ClustalW::Report)
new (Bio::PhyloXML::DomainArchitecture)
new (Bio::TRANSFAC::CLASS)
new (Bio::References)
new (Bio::TRANSFAC::MATRIX)
new (Bio::References)
new (Bio::SQL::Sequence)
new (Bio::PDB::DataType::Pdb_String)
new (Bio::KEGG::ORTHOLOGY)
new (Bio::PDB::DataType::Pdb_SList)
new (Bio::Taxonomy)
new (Bio::PDB::DataType::Pdb_Real)
new (Bio::PDB::DataType::Pdb_List)
new (Bio::FlatFileIndex::FileID)
new (Bio::Spidey::Report::Segment)
new (Bio::Ensembl)
new (Bio::MAFFT::Report)
new (Bio::Sequence::NA::MidiTrack)
new (Bio::ClustalW)
new (Bio::PhyloXML::BinaryCharacters)
new (Bio::PTS1::Report)
new (Bio::SOFT)
new (Bio::TRANSFAC)
new (Bio::TMHMM::TMH)
new (Bio::FlatFileIndex::Template::NameSpace)
new (Bio::TMHMM::Report)
new (Bio::RestrictionEnzyme::Range::SequenceRange::Fragments)
new (Bio::PhyloXML::Distribution)
new (Bio::Alignment)
new (Bio::FlatFile::AutoDetect::RuleRegexp)
new (Bio::Blast)
new (Bio::PTS1)
new (Bio::FlatFile::AutoDetect::RuleProc)
new (Bio::FlatFile::AutoDetect::RuleDebug)
new (Bio::PDB::Residue)
new (Bio::FlatFile::AutoDetect::RuleRegexp2)
new (Bio::Sim4)
new (Bio::FANTOM::MaXML)
new (Bio::FlatFile::AutoDetect::RuleTemplate)
new (Bio::PSORT::CGIDriver)
new (Bio::PSORT::PSORT2::Remote)
new (Bio::PhyloXML::Node)
new (Bio::DAS::SEGMENT)
new (Bio::Sim4::Report)
new (Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair)
new (Bio::KEGG::GENOME)
new (Bio::GFF::GFF2::Record::Value)
new (Bio::Command::Tmpdir)
new (Bio::FlatFileIndex::Flat_1::Record)
new (Bio::PSORT::PSORT2::Report)
new (Bio::Sim4::Report::SegmentPair)
new (Bio::GFF::GFF2::MetaData)
new (Bio::PSORT::PSORT2)
new (Bio::PDB::ChemicalComponent)
new (Bio::MAFFT)
new (Bio::FlatFile::AutoDetect)
new (Bio::PSORT::PSORT1::Remote)
new (Bio::PSORT::PSORT1::Report)
new (Bio::PhyloXML::Sequence)
new (Bio::RestrictionEnzyme::DoubleStranded::CutLocations)
new (Bio::PhyloXML::Annotation)
new (Bio::PhyloXML::Polygon)
new (Bio::Sim4::Report::SeqDesc)
new (Bio::PDB::Model)
new (Bio::Sim4::Report::Hit)
new (Bio::GFF::GFF3)
new (Bio::GFF::GFF3::SequenceRegion)
new (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
new (Bio::FlatFile::BufferedInputStream)
new (Bio::PhyloXML::Tree)
new (Bio::PSORT::PSORT1)
new (Bio::PDB::Chain)
new (Bio::FlatFile::Splitter::Template)
new (Bio::PhyloXML::Other)
new (Bio::FlatFile::Splitter::LineOriented)
new (Bio::Tree::Node)
new (Bio::FlatFile::Splitter::Default)
new (Bio::NCBIDB::Common)
new (Bio::GFF::GFF3::Record)
new (Bio::NCBIDB)
new (Bio::SiRNA::Pair)
new (Bio::Sim4::Report::Segment)
new (Bio::Feature)
new (Bio::PhyloXML::Writer)
new (Bio::RestrictionEnzyme::DoubleStranded)
new (Bio::KEGG::API)
new (Bio::Tree::Edge)
new (Bio::Fasta::Report::Hit::Query)
new (Bio::FlatFile)
new (Bio::Feature::Qualifier)
new (Bio::GFF::GFF3::Record::Gap)
new (Bio::GFF::GFF3::Record::Target)
new (Bio::RestrictionEnzyme::Range::SequenceRange::Fragment)
new (Bio::SiRNA::ShRNA)
new (Bio::PhyloXML::Taxonomy)
new (Bio::DAS::GFF)
new (Bio::SiRNA)
new (Bio::KEGG::DRUG)
new (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
new (Bio::FlatFileIndex::Indexer::NameSpace)
new (Bio::Blast::Default::Report::Hit)
new (Bio::FlatFileIndex)
new (Bio::KEGG::ENZYME)
new (Bio::Location)
new (Bio::Genscan::Report::Gene)
new (Bio::FlatFileIndex::Indexer::NameSpaces)
new (Bio::Blast::Default::Report::HSP)
new (Bio::PROSITE)
new (Bio::Meme::Motif)
new (Bio::SOAPWSDL)
new (Bio::Blast::Default::Report)
new (Bio::SOSUI::Report::TMH)
new (Bio::Genscan::Report::Exon)
new (Bio::Genscan::Report)
new (Bio::Fasta::Report::Hit)
new (Bio::FlatFileIndex::Indexer::Parser)
new (Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser)
new (Bio::FlatFileIndex::Indexer::Parser::SPTRParser)
new (Bio::FlatFileIndex::Indexer::Parser::GenBankParser)
new (Bio::Fasta::Report::FastaFormat10Splitter)
new (Bio::FlatFileIndex::Indexer::Parser::GenPeptParser)
new (Bio::MEDLINE)
new (Bio::EBI::SOAP)
new (Bio::GenPept::Locus)
new (Bio::Fasta::Report::Program)
new (Bio::GCG::Msf)
new (Bio::AAindex2)
new (Bio::Lasergene)
new (Bio::HGC::HiGet)
new (Bio::DDBJ::XML)
new (Bio::KEGG::COMPOUND)
new (Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser)
new (Bio::FastaFormat)
new (Bio::Meme::Mast)
new (Bio::FlatFileIndex::Indexer::Parser::TemplateParser)
new (Bio::Meme::Mast::Report)
new (Bio::Fasta::Report)
new (Bio::Abif)
new (Bio::NBRF)
new (Bio::GFF::Record)
new (Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser)
new (Bio::RestrictionEnzyme)
new (Bio::DDBJ::XML::RequestManager)
new (Bio::FlatFileIndex::Indexer::Parser::EMBLParser)
new (Bio::GFF::GFF3::RecordBoundary)
new (Bio::KEGG::BRITE)
new (Bio::FANTOM::MaXML::Annotation::DataSrc)
new (Bio::Fasta)
new (Bio::KEGG::EXPRESSION)
new (Bio::FlatFile::AutoDetect::RuleSpecial)
new (Bio::KEGG::REACTION)
new (Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser)
new (Bio::NCBI::SOAP)
new (Bio::CodonTable)
new (Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser)
new (Bio::PDB::DataType::Pdb_Integer)
new2 (Bio::Alignment)
new2 (Bio::MAFFT)
new2 (Bio::Alignment::OriginalAlignment)
new_direct (Bio::PDB::Record)
new_from_sequences_na (Bio::GFF::GFF3::Record::Gap)
new_from_sequences_na_aa (Bio::GFF::GFF3::Record::Gap)
new_from_string (Bio::FlatFileIndex::FileID)
new_http (Bio::Command)
new_inherit (Bio::PDB::Record)
new_intron (Bio::Spidey::Report::SegmentPair)
new_with_fungi_function (Bio::PTS1)
new_with_general_function (Bio::PTS1)
new_with_metazoa_function (Bio::PTS1)
newick (Bio::Tree)
next_entry (Bio::FlatFile)
next_tree (Bio::PhyloXML::Parser)
nhx_parameters (Bio::Tree::Node)
nhx_parameters (Bio::Tree::Edge)
nid (Bio::NCBIDB::Common)
nodes (Bio::Pathway)
nodes (Bio::Tree)
normalize (Bio::Alignment::OriginalAlignment)
normalize! (Bio::Alignment::EnumerableExtension)
normalize! (Bio::Blast::NCBIOptions)
normalize! (Bio::Sequence::Common)
notes (Bio::Blast::WU::Report)
notice (Bio::Blast::WU::Report)
nr (Bio::PROSITE)
ntlen (Bio::KEGG::GENES)
ntseq (Bio::EMBL)
ntseq (Bio::KEGG::GENES)
nucleotide_databases (Bio::Blast::Remote::Information)
num_gene (Bio::KEGG::GENOME)
num_hits (Bio::Sim4::Report)
num_hits (Bio::Blat::Report)
num_hits (Bio::Spidey::Report)
num_rna (Bio::KEGG::GENOME)
number_of_edges (Bio::Tree)
number_of_exons (Bio::Spidey::Report::Hit)
number_of_nodes (Bio::Tree)
number_of_sequences (Bio::Alignment::EnumerableExtension)
number_of_sequences (Bio::Alignment::OriginalAlignment)
number_of_sequences (Bio::Alignment::HashExtension)
number_of_sequences (Bio::Alignment::ArrayExtension)
number_of_splice_sites (Bio::Spidey::Report::Hit)
nwap (Bio::MAFFT)
nwns (Bio::MAFFT)
nwnsi (Bio::MAFFT)
object_file (Bio::Shell::Core)
obsolete? (Bio::KEGG::ENZYME)
oc (Bio::TRANSFAC)
oc (Bio::EMBLDB::Common)
og (Bio::EMBLDB::Common)
oh (Bio::SPTR)
okazaki (Bio::PSORT::PSORT2)
okazaki (Bio::PSORT::PSORT1)
old_matrix (Bio::AAindex2)
omim (Bio::NCBI::REST::EFetch::Methods)
one (Bio::AminoAcid::Data)
one2name (Bio::AminoAcid::Data)
one2three (Bio::AminoAcid::Data)
open (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
open (Bio::FlatFileIndex::BDBwrapper)
open (Bio::FlatFileIndex::DataBank)
open (Bio::FlatFileIndex)
open (Bio::DB)
open (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
open (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
open (Bio::FlatFile)
open (Bio::Blast::Default::Report)
open (Bio::SangerChromatogram)
open (Bio::PhyloXML::Parser)
open (Bio::FlatFileIndex::FileID)
open (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
open_file (Bio::FlatFile)
open_file (Bio::FlatFile::BufferedInputStream)
open_flatfile (Bio::FlatFileIndex::Indexer::Parser::TemplateParser)
open_flatfile (Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser)
open_flatfile (Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser)
open_flatfile (Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser)
open_history (Bio::Shell::Ghost)
open_uri (Bio::PhyloXML::Parser)
open_uri (Bio::FlatFile::BufferedInputStream)
open_uri (Bio::FlatFile)
opening_splash (Bio::Shell::Ghost)
option (Bio::HMMER)
option (Bio::Blast)
option (Bio::MAFFT)
option (Bio::Sim4)
option (Bio::ClustalW)
option (Bio::Fasta)
option= (Bio::Fasta)
option= (Bio::HMMER)
option= (Bio::Blast)
options (Bio::PAML::Codeml)
options (Bio::Blast::NCBIOptions)
options= (Bio::Blast)
options= (Bio::PAML::Codeml)
order (Bio::Alignment::OriginalAlignment)
org_class (Bio::TRANSFAC)
org_species (Bio::TRANSFAC)
organism (Bio::KEGG::GENOME)
organism (Bio::SQL::Sequence)
organism (Bio::KEGG::GENES)
organism (Bio::NCBIDB::Common)
organism= (Bio::SQL::Sequence)
organisms (Bio::KEGG::Taxonomy)
orientation (Bio::RestrictionEnzyme::SingleStrandComplement)
orientation (Bio::RestrictionEnzyme::SingleStrand)
origin (Bio::NCBIDB::Common)
original_data (Bio::PDB::Record)
original_db (Bio::KEGG::GENOME)
orthologs (Bio::KEGG::GENES)
orthologs (Bio::KEGG::REACTION)
orthologs (Bio::KEGG::ENZYME)
orthologs (Bio::KEGG::GLYCAN)
orthologs_as_hash (Bio::KEGG::Common::OrthologsAsHash)
orthologs_as_hash (Bio::KEGG::GLYCAN)
orthologs_as_hash (Bio::KEGG::GENES)
orthologs_as_hash (Bio::KEGG::REACTION)
orthologs_as_hash (Bio::KEGG::ENZYME)
orthologs_as_strings (Bio::KEGG::GLYCAN)
orthologs_as_strings (Bio::KEGG::GENES)
orthologs_as_strings (Bio::KEGG::ENZYME)
orthologs_as_strings (Bio::KEGG::REACTION)
os (Bio::EMBLDB::Common)
os (Bio::SPTR)
os (Bio::TRANSFAC)
other_seqids (Bio::SQL::Sequence)
out (Bio::FlatFileIndex::DEBUG)
out= (Bio::FlatFileIndex::DEBUG)
out_degree (Bio::Tree)
out_edges (Bio::Tree)
output (Object)
output (Bio::Alignment::Output)
output (Bio::Shell::ColoredCodonTable)
output (Bio::Sequence::Format::Formatter::Fasta_numeric)
output (Bio::Sequence::Format::FormatterBase)
output (Bio::Sequence::Format::FormatterBase)
output (Bio::Sequence::Format::Formatter::Fasta_ncbi)
output (Bio::Sequence::Format)
output (Bio::Sequence::Format::Formatter::Fasta)
output (Bio::Sequence::Format::Formatter::Raw)
output (Bio::Tree)
output (Bio::Sequence::Format::Formatter::Fastq)
output (Bio::Iprscan::Report)
output_clustal (Bio::Alignment::Output)
output_fasta (Bio::Alignment::Output)
output_molphy (Bio::Alignment::Output)
output_msf (Bio::Alignment::Output)
output_newick (Bio::Tree)
output_nhx (Bio::Tree)
output_phylip (Bio::Alignment::Output)
output_phylip_distance_matrix (Bio::Tree)
output_phylipnon (Bio::Alignment::Output)
overlap (Bio::Blast::Report::Hit)
overlap (Bio::Blast::Default::Report::Hit)
overlap (Bio::Fasta::Report::Hit)
ox (Bio::SPTR)
p2q (Bio::Sequence::QualityScore::Phred)
p2q (Bio::Sequence::QualityScore::Solexa)
pa (Bio::PROSITE)
pa2re (Bio::PROSITE)
pa2re (Bio::PROSITE)
pages (Bio::MEDLINE)
palindromic? (Bio::RestrictionEnzyme::SingleStrand)
parameter_matrix (Bio::Blast::WU::Report)
parameters (Bio::Blast::WU::Report)
parent (Bio::Tree)
parse (Bio::GFF::GFF3::Record::Target)
parse (Bio::GFF::GFF2::MetaData)
parse (Bio::Blast::NCBIOptions)
parse (Bio::GFF::GFF3::SequenceRegion)
parse (Bio::Sim4::Report::SeqDesc)
parse (Bio::Spidey::Report::SegmentPair)
parse (Bio::Sim4::Report::SegmentPair)
parse (Bio::Spidey::Report::SeqDesc)
parse (Bio::GFF::GFF2)
parse (Bio::GFF::GFF2::Record)
parse (Bio::GFF::GFF3::Record)
parse (Bio::GFF::GFF3::Record)
parse (Bio::GFF::GFF3::Record::Gap)
parse (Bio::GFF::GFF2::Record)
parse (Bio::GFF::GFF3)
parse_embl_DR_line (Bio::Sequence::DBLink)
parse_enzymes (Bio::REBASE)
parse_goids (Bio::GO::Ontology)
parse_primary (Bio::FlatFileIndex::Indexer::Parser::TemplateParser)
parse_primary (Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser)
parse_ptxt (Bio::Iprscan::Report)
parse_ptxt_entry (Bio::Iprscan::Report)
parse_raw (Bio::Iprscan::Report)
parse_raw_entry (Bio::Iprscan::Report)
parse_references (Bio::REBASE)
parse_secondary (Bio::FlatFileIndex::Indexer::Parser::TemplateParser)
parse_suppliers (Bio::REBASE)
parse_txt (Bio::Iprscan::Report)
parse_txt_entry (Bio::Iprscan::Report)
parse_uniprot_DR_line (Bio::Sequence::DBLink)
parser (Bio::GO::GeneAssociation)
parser (Bio::GO::External2go)
parser (Bio::PSORT::PSORT1::Report)
parser (Bio::Genscan::Report::Exon)
parser (Bio::PSORT::PSORT2::Report)
parser (Bio::Fasta)
partial (Bio::PROSITE)
path (Bio::Tree)
path (Bio::Command::Tmpdir)
path (Bio::KEGG::Keggtab)
path (Bio::FlatFile)
pathway (Bio::KEGG::GENES)
pathways (Bio::KEGG::COMPOUND)
pathways (Bio::KEGG::GENES)
pathways (Bio::KEGG::REACTION)
pathways (Bio::KEGG::DRUG)
pathways (Bio::KEGG::ORTHOLOGY)
pathways (Bio::KEGG::ENZYME)
pathways (Bio::KEGG::GLYCAN)
pathways_as_hash (Bio::KEGG::Common::PathwaysAsHash)
pathways_as_hash (Bio::KEGG::REACTION)
pathways_as_hash (Bio::KEGG::DRUG)
pathways_as_hash (Bio::KEGG::COMPOUND)
pathways_as_hash (Bio::KEGG::GLYCAN)
pathways_as_hash (Bio::KEGG::ENZYME)
pathways_as_hash (Bio::KEGG::GENES)
pathways_as_strings (Bio::KEGG::ENZYME)
pathways_as_strings (Bio::KEGG::GENES)
pathways_as_strings (Bio::KEGG::DRUG)
pathways_as_strings (Bio::KEGG::COMPOUND)
pathways_as_strings (Bio::KEGG::REACTION)
pathways_as_strings (Bio::KEGG::GLYCAN)
pattern (Bio::PROSITE)
pattern (Bio::Blast::Default::Report::Iteration)
pattern (Bio::Blast::Default::Report)
pattern (Bio::RestrictionEnzyme::SingleStrand)
pattern (Bio::Blast::Report)
pattern_positions (Bio::Blast::Default::Report)
pattern_positions (Bio::Blast::Default::Report::Iteration)
pdb (Bio::Shell::Demo)
pdb_hetdic (Bio::Shell::Demo)
pdb_xref (Bio::PROSITE)
pdoc_xref (Bio::PROSITE)
peking (Bio::PSORT::PSORT1)
peking (Bio::PSORT::PSORT2)
percent_identity (Bio::Blat::Report::Hit)
percent_identity (Bio::Spidey::Report::Hit)
percent_identity (Bio::Blast::Report::Hit)
permission (Bio::FlatFileIndex::BDBdefault)
permute (Bio::RestrictionEnzyme::Analysis)
pg (Bio::MEDLINE)
phred_p2q (Bio::Sequence::QualityScore::Phred)
phred_q2p (Bio::Sequence::QualityScore::Phred)
pii (Bio::MEDLINE)
plasmids (Bio::KEGG::GENOME)
plugin_dir (Bio::Shell::Core)
pmc (Bio::NCBI::REST::EFetch::Methods)
pmfetch (Bio::PubMed)
pmfetch (Bio::PubMed)
pmid (Bio::MEDLINE)
pos (Bio::FlatFile)
pos (Bio::FlatFile::BufferedInputStream)
pos= (Bio::FlatFile)
pos= (Bio::FlatFile::BufferedInputStream)
position (Bio::KEGG::GENES)
positions_on (Bio::Map::ActsLikeMarker)
positive (Bio::PROSITE)
positive_hits (Bio::PROSITE)
positive_sequences (Bio::PROSITE)
post_form (Bio::Command)
prefetch_buffer (Bio::FlatFile::BufferedInputStream)
prefetch_gets (Bio::FlatFile::BufferedInputStream)
prefetch_readpartial (Bio::FlatFile::BufferedInputStream)
present_count= (Bio::PhyloXML::BinaryCharacters)
primary (Bio::RestrictionEnzyme::DoubleStranded::CutLocations)
primary (Bio::FlatFileIndex::DataBank)
primary (Bio::RestrictionEnzyme::Fragments)
primary= (Bio::FlatFileIndex::DataBank)
primary_accession (Bio::SQL::Sequence)
primary_accession= (Bio::SQL::Sequence)
primary_namespace (Bio::FlatFileIndex)
primary_to_array_index (Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation)
print (Bio::FlatFileIndex::DEBUG)
process (Bio::Lasergene)
process (Bio::SOFT)
process_sequences_na (Bio::GFF::GFF3::Record::Gap)
process_sequences_na_aa (Bio::GFF::GFF3::Record::Gap)
products (Bio::KEGG::ENZYME)
products (Bio::KEGG::DRUG)
profile (Bio::PROSITE)
program (Bio::Blast::Default::Report)
project_workdir (BiorubyHelper)
protein? (Bio::Blat::Report::Hit)
protein_databases (Bio::Blast::Remote::Information)
protein_name (Bio::SPTR)
pt (Bio::MEDLINE)
publication_type (Bio::MEDLINE)
pubmed (Bio::NCBI::REST::EFetch::Methods)
pubmed_url (Bio::Reference)
purge (Bio::Alignment::OriginalAlignment)
push (Bio::Sequence::NA::MidiTrack)
push_silent (Bio::Sequence::NA::MidiTrack)
put_record (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
q2p (Bio::Sequence::QualityScore::Phred)
q2p (Bio::Sequence::QualityScore::Solexa)
qseq (Bio::Spidey::Report::SegmentPair)
qseq (Bio::Sim4::Report::SegmentPair)
qualities (Bio::Fastq)
quality_score_type (Bio::Sequence::QualityScore::Phred)
quality_score_type (Bio::Fastq)
quality_score_type (Bio::Sequence::QualityScore::Solexa)
quality_scores (Bio::Fastq)
query (Bio::Hinv::KeywordSearch)
query (Bio::Registry)
query (Bio::Blast)
query (Bio::Hinv::IdSearch)
query (Bio::ClustalW)
query (Bio::FastaFormat)
query (Bio::Hinv::Common)
query (Bio::Fasta)
query (Bio::Fetch)
query (Bio::FANTOM)
query (Bio::MAFFT)
query (Bio::HMMER)
query (Bio::PAML::Codeml)
query (Bio::Blat::Report::Hit)
query (Bio::PAML::Common)
query (Bio::Alignment::FactoryTemplate::Simple)
query (Bio::PubMed)
query (Bio::PubMed)
query (Bio::Sim4)
query (Bio::PAML::Yn00)
query_align (Bio::Alignment::FactoryTemplate::Simple)
query_align (Bio::MAFFT)
query_align (Bio::ClustalW)
query_alignment (Bio::MAFFT)
query_alignment (Bio::ClustalW)
query_alignment (Bio::Alignment::FactoryTemplate::Simple)
query_by_filename (Bio::MAFFT)
query_by_filename (Bio::Alignment::FactoryTemplate::Simple)
query_by_filename (Bio::ClustalW)
query_by_string (Bio::PAML::Common)
query_by_string (Bio::PAML::Yn00)
query_by_string (Bio::PAML::Codeml)
query_command (Bio::Command)
query_command_fork (Bio::Command)
query_command_open3 (Bio::Command)
query_command_popen (Bio::Command)
query_def (Bio::Blat::Report::Hit)
query_def (Bio::Sim4::Report)
query_def (Bio::Blat::Report)
query_def (Bio::Spidey::Report)
query_def (Bio::Blast::Default::Report)
query_def (Bio::Blast::RPSBlast::Report)
query_def (Bio::Fasta::Report::Hit)
query_def (Bio::Spidey::Report::Hit)
query_def (Bio::Sim4::Report::Hit)
query_end (Bio::Blast::Default::Report::Hit)
query_end (Bio::Fasta::Report::Hit)
query_end (Bio::Blast::Report::Hit)
query_from (Bio::HMMER::Report::Hsp)
query_from (Bio::Spidey::Report::SegmentPair)
query_from (Bio::Sim4::Report::SegmentPair)
query_id (Bio::Spidey::Report)
query_id (Bio::Sim4::Report::Hit)
query_id (Bio::Blat::Report)
query_id (Bio::Blat::Report::Hit)
query_id (Bio::Spidey::Report::Hit)
query_id (Bio::Fasta::Report::Hit)
query_id (Bio::Sim4::Report)
query_id (Bio::Iprscan::Report::Match)
query_len (Bio::Blast::RPSBlast::Report)
query_len (Bio::Sim4::Report)
query_len (Bio::Blat::Report::Hit)
query_len (Bio::TargetP::Report)
query_len (Bio::Sim4::Report::Hit)
query_len (Bio::Blast::Default::Report)
query_len (Bio::Spidey::Report)
query_len (Bio::Fasta::Report::Hit)
query_len (Bio::Spidey::Report::Hit)
query_len (Bio::Blat::Report)
query_pairwise (Bio::Sim4)
query_record_number (Bio::Blast::WU::Report)
query_seq (Bio::Blast::Default::Report::Hit)
query_seq (Bio::Fasta::Report::Hit)
query_seq (Bio::Blast::Report::Hit)
query_seq (Bio::HMMER::Report::Hsp)
query_start (Bio::Fasta::Report::Hit)
query_start (Bio::Blast::Report::Hit)
query_start (Bio::Blast::Default::Report::Hit)
query_strand (Bio::Spidey::Report::SegmentPair)
query_string (Bio::ClustalW)
query_string (Bio::MAFFT)
query_string (Bio::Alignment::FactoryTemplate::Simple)
query_to (Bio::Spidey::Report::SegmentPair)
query_to (Bio::Sim4::Report::SegmentPair)
query_to (Bio::HMMER::Report::Hsp)
query_type (Bio::Fasta::Report::Hit)
ra (Bio::TRANSFAC)
rad2deg (Bio::PDB::Utils)
randomize (Bio::Sequence::NA)
randomize (Bio::Sequence::Common)
randomize (Bio::Sequence::AA)
range (Bio::Location)
range (Bio::Genscan::Report::Exon)
range (Bio::Locations)
raw= (Bio::FlatFile)
raw_to_reference (Bio::REBASE)
rc (Bio::TargetP::Report)
rcode (Bio::Sequence::NA::MidiTrack)
rd (Bio::Reference)
re (Bio::TRANSFAC::SITE)
re (Bio::PROSITE)
re_cut_symbol (Bio::RestrictionEnzyme::CutSymbol)
re_cut_symbol_adjacent (Bio::RestrictionEnzyme::CutSymbol)
reaction (Bio::KEGG::ENZYME)
reactions (Bio::KEGG::COMPOUND)
reactions (Bio::KEGG::GLYCAN)
read (Bio::Sequence)
read (Bio::FlatFileIndex::DataBank)
read (Bio::REBASE)
read (Bio::FlatFileIndex::FileID)
read_uri (Bio::Command)
readfiles (Bio::Alignment::OriginalAlignment)
readfiles (Bio::Alignment)
rebase (Bio::RestrictionEnzyme)
recalc (Bio::FlatFileIndex::FileIDs)
recalc (Bio::FlatFileIndex::FileID)
recalc_all (Bio::FlatFileIndex::FileIDs)
record (Bio::PDB::ChemicalComponent)
record (Bio::PDB)
record_name (Bio::PDB::Record)
record_size (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
record_type (Bio::PDB::Record)
records (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
records (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
red= (Bio::PhyloXML::BranchColor)
reduce (Bio::KEGG::Taxonomy)
ref (Bio::EMBLDB::Common)
ref (Bio::SPTR)
ref_authors (Bio::TRANSFAC)
ref_data (Bio::TRANSFAC)
ref_no (Bio::TRANSFAC)
ref_title (Bio::TRANSFAC)
reference (Bio::MEDLINE)
reference (Bio::Blast::Default::Report)
reference (Bio::LITDB)
reference= (Bio::SQL::Sequence)
reference_link (BiorubyHelper)
references (Bio::SPTR)
references (Bio::Blast::Default::Report)
references (Bio::KEGG::GLYCAN)
references (Bio::EMBLDB::Common)
references (Bio::KEGG::GENOME)
references (Bio::NCBIDB::Common)
references (Bio::SQL::Sequence)
region (Bio::DAS::SEGMENT)
regulated (Bio::KEGG::EXPRESSION)
rehash (Bio::PDB::Model)
rehash (Bio::Alignment::OriginalAlignment)
rehash (Bio::PDB::Chain)
rehash (Bio::FlatFile::AutoDetect)
rehash_heterogens (Bio::PDB::Chain)
rehash_residues (Bio::PDB::Chain)
relative (Bio::Locations)
release (Bio::PROSITE)
release_created (Bio::EMBL)
release_modified (Bio::EMBL)
reload_script (BiorubyController)
remark (Bio::KEGG::COMPOUND)
remark (Bio::KEGG::GLYCAN)
remark (Bio::PDB)
remark (Bio::KEGG::DRUG)
remote (Bio::Blast)
remote (Bio::PSORT::PSORT2)
remote (Bio::Fasta)
removeSolvent (Bio::PDB::Model)
remove_all_gaps (Bio::Alignment::OriginalAlignment)
remove_all_gaps! (Bio::Alignment::EnumerableExtension)
remove_edge (Bio::Tree)
remove_edge_if (Bio::Tree)
remove_entry_secure (Bio::Command)
remove_gaps! (Bio::Alignment::SiteMethods)
remove_incomplete_cuts (Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts)
remove_node (Bio::Tree)
remove_node_if (Bio::Tree)
remove_nonsense_nodes (Bio::Tree)
remove_seq (Bio::Alignment::OriginalAlignment)
render_log (BiorubyHelper)
rep_accession_no (Bio::Hinv::HixRepresent)
rep_h_invitational_id (Bio::Hinv::HixRepresent)
rep_match (Bio::Blat::Report::Hit)
reparse (Bio::Newick)
replace (Bio::Location)
replace_attributes (Bio::GFF::GFF2::Record)
replace_slice (Bio::Alignment::OriginalAlignment)
report (Bio::SiRNA::Pair)
report (Bio::SiRNA::ShRNA)
reports (Bio::Blast)
reports (Bio::TMHMM)
reports (Bio::HMMER)
reports_xml (Bio::Blast)
representative_annotations (Bio::FANTOM::MaXML::Cluster)
representative_clone (Bio::FANTOM::MaXML::Cluster)
representative_cloneid (Bio::FANTOM::MaXML::Cluster)
representative_seqid (Bio::FANTOM::MaXML::Cluster)
representative_sequence (Bio::FANTOM::MaXML::Cluster)
resSeq= (Bio::PDB::Residue)
reset (Bio::Alignment::FactoryTemplate::Simple)
reset (Bio::Blast::Remote::Information)
reset (Bio::ClustalW)
reset (Bio::Alignment::FactoryTemplate::FileInFileOutWithTree)
reset (Bio::MAFFT)
reset_entrez_default_parameters (Bio::NCBI)
residues (Bio::PDB::ResidueFinder)
restore (Bio::Shell::Web::Results)
result (Bio::Hinv::HitPubmedId)
result (Bio::Hinv::HitCnt)
result (Bio::Hinv::HitDefinition)
result (Bio::Hinv::HitXML)
result (Bio::Hinv::KeywordSearch)
result (Bio::Hinv::Acc2hit)
result (Bio::Hinv::HixCnt)
result (Bio::Hinv::Hit2acc)
result (Bio::Hinv::HixRepresent)
result (Bio::Hinv::Hix2hit)
results (BiorubyController)
retrieve (Bio::TogoWS::REST)
retrieve (Bio::TogoWS::REST)
reverse_complement (Bio::Sequence::NA)
reverse_complement! (Bio::Sequence::NA)
revtrans (Bio::CodonTable)
rewind (Bio::FlatFile)
rewind (Bio::FlatFile::BufferedInputStream)
rewind (Bio::Blast::Report::BlastXmlSplitter)
rewind (Bio::FlatFile::Splitter::Template)
rewind (Bio::FlatFile::Splitter::LineOriented)
rewind (Bio::Blast::RPSBlast::RPSBlastSplitter)
rexml (Bio::Blast::Report)
reynolds (Bio::SiRNA)
reynolds? (Bio::SiRNA)
right_padding (Bio::RestrictionEnzyme::StringFormatting)
rl (Bio::TRANSFAC)
rn (Bio::TRANSFAC)
rna (Bio::Sequence::NA)
rna! (Bio::Sequence::NA)
rna? (Bio::Sequence::NA)
row_sum (Bio::ContingencyTable)
row_sum_all (Bio::ContingencyTable)
rows (Bio::AAindex2)
rpairs (Bio::KEGG::REACTION)
rpairs (Bio::KEGG::COMPOUND)
rpairs_as_hash (Bio::KEGG::REACTION)
rpairs_as_strings (Bio::KEGG::REACTION)
rpairs_as_tokens (Bio::KEGG::REACTION)
rstrip (Bio::Alignment::OriginalAlignment)
rstrip! (Bio::Alignment::EnumerableExtension)
rt (Bio::TRANSFAC)
ru (Bio::PROSITE)
rule (Bio::PROSITE)
run (Bio::PAML::Common)
run (Bio::Meme::Mast)
run (Bio::EMBOSS)
s1 (Bio::TRANSFAC::SITE)
safe_command_line_array (Bio::Command)
save (Bio::SQL::Sequence)
save_config (Bio::Shell::Ghost)
save_config_file (Bio::Shell::Ghost)
save_history (Bio::Shell::Ghost)
save_history_file (Bio::Shell::Ghost)
save_image (Bio::KEGG::API)
save_object (Bio::Shell::Ghost)
save_object_file (Bio::Shell::Ghost)
save_script (Bio::Shell::Ghost)
save_script_file (Bio::Shell::Ghost)
save_session (Bio::Shell::Ghost)
save_yaml (Bio::REBASE)
sc (Bio::TRANSFAC::FACTOR)
sc_match (Bio::Blast::Report)
sc_mismatch (Bio::Blast::Report)
science (Bio::Reference)
score (Bio::Blast::Default::Report::Hit)
score (Bio::Blat::Report::Hit)
score (Bio::Blast::WU::Report::Hit)
scores2str (Bio::Fastq::FormatData)
script (Bio::Shell::Ghost)
script_begin (Bio::Shell::Ghost)
script_dir (Bio::Shell::Core)
script_end (Bio::Shell::Ghost)
script_file (Bio::Shell::Core)
sd (Bio::TRANSFAC::GENE)
sd (Bio::TRANSFAC::CLASS)
search (Bio::TogoWS::REST)
search (Bio::PubMed)
search (Bio::FlatFileIndex::NameSpaces)
search (Bio::FlatFileIndex)
search (Bio::FlatFileIndex::Flat_1::SecondaryNameSpace)
search (Bio::NCBI::REST::ESearch::Methods)
search (Bio::FlatFileIndex::Template::NameSpace)
search (Bio::FlatFileIndex::BDB_1::SecondaryNameSpace)
search (Bio::TogoWS::REST)
search (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
search (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
search (Bio::PubMed)
search (Bio::FlatFileIndex::BDB_1::PrimaryNameSpace)
search_all (Bio::FlatFileIndex::DataBank)
search_all_get_unique_id (Bio::FlatFileIndex::DataBank)
search_database_list (Bio::TogoWS::REST)
search_database_list (Bio::TogoWS::REST)
search_names (Bio::FlatFileIndex::NameSpaces)
search_namespaces (Bio::FlatFileIndex::DataBank)
search_namespaces (Bio::FlatFileIndex)
search_namespaces_get_unique_id (Bio::FlatFileIndex::DataBank)
search_primary (Bio::FlatFileIndex)
search_primary (Bio::FlatFileIndex::DataBank)
search_primary_get_unique_id (Bio::FlatFileIndex::DataBank)
secondary (Bio::FlatFileIndex::DataBank)
secondary= (Bio::FlatFileIndex::DataBank)
secondary_namespaces (Bio::FlatFileIndex)
seek (Bio::FlatFileIndex::FileID)
seek (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
segment (Bio::NCBIDB::Common)
segmentpairs (Bio::Sim4::Report::Hit)
segmentpairs (Bio::Spidey::Report::Hit)
select (Bio::Alignment::OriginalAlignment)
seq (Bio::DBGET)
seq (Bio::FastaFormat)
seq (Bio::EMBL)
seq (Bio::SangerChromatogram)
seq (Bio::GenPept)
seq (Bio::SPTR)
seq (Bio::Fastq)
seq (Bio::NBRF)
seq (Bio::GenBank)
seq (Bio::Lasergene)
seq (Bio::SQL::Sequence)
seq (Bio::Sequence::Common)
seq (Bio::GCG::Seq)
seq! (Bio::Sequence::Common)
seq1_intron (Bio::Sim4::Report::SegmentPair)
seq2 (Bio::DBGET)
seq2_intron (Bio::Sim4::Report::SegmentPair)
seq= (Bio::SQL::Sequence)
seq_class (Bio::NBRF)
seq_data (Bio::GCG::Msf)
seq_len (Bio::GenPept)
seq_len (Bio::GenBank)
seq_length (Bio::Alignment::EnumerableExtension)
seqclass (Bio::Alignment::EnumerableExtension)
seqclass (Bio::Alignment::PropertyMethods)
seqlen (Bio::EMBL)
seqres (Bio::PDB)
seqret (Bio::EMBOSS)
sequence (Bio::NCBI::REST::EFetch::Methods)
sequence (Bio::Shell::Demo)
sequence (Bio::FANTOM::MaXML::Cluster)
sequence (Bio::SQL::Location)
sequence (Bio::SQL::Seqfeature)
sequence_length (Bio::EMBL)
sequence_length (Bio::SPTR)
sequence_names (Bio::Alignment::HashExtension)
sequence_names (Bio::Alignment::EnumerableExtension)
sequence_string (Bio::SangerChromatogram)
sequence_version (Bio::SQL::Sequence)
sequence_version= (Bio::SQL::Sequence)
sequences (Bio::FANTOM::MaXML::Cluster)
server= (Bio::Blast)
server_uri (Bio::Ensembl)
session_dir (Bio::Shell::Core)
set (Bio::Blast::NCBIOptions)
set_RN (Bio::SPTR)
set_aaseq (Bio::Genscan::Report::Gene)
set_alignment (Bio::HMMER::Report::Hsp)
set_all_property (Bio::Alignment::PropertyMethods)
set_attribute (Bio::GFF::GFF2::Record)
set_cut_symbol (Bio::RestrictionEnzyme::CutSymbol)
set_datatype (Bio::Nexus::CharactersBlock)
set_date (Bio::GO::External2go)
set_default_parameters (Bio::PAML::Common)
set_desc (Bio::GO::External2go)
set_features (Bio::PSORT::PSORT2::Report)
set_gap_character (Bio::Nexus::CharactersBlock)
set_header_line (Bio::PSORT::PSORT2::Report)
set_kNN_prob (Bio::PSORT::PSORT2::Report)
set_match_character (Bio::Nexus::CharactersBlock)
set_matrix (Bio::Nexus::CharactersBlock)
set_matrix (Bio::Nexus::DistancesBlock)
set_missing (Bio::Nexus::CharactersBlock)
set_naseq (Bio::Genscan::Report::Gene)
set_number_of_characters (Bio::Nexus::DistancesBlock)
set_number_of_characters (Bio::Nexus::CharactersBlock)
set_number_of_taxa (Bio::Nexus::CharactersBlock)
set_number_of_taxa (Bio::Nexus::TaxaBlock)
set_number_of_taxa (Bio::Nexus::DistancesBlock)
set_polyA (Bio::Genscan::Report::Gene)
set_prediction (Bio::PSORT::PSORT2::Report)
set_primary_namespace (Bio::FlatFileIndex::Indexer::Parser::TemplateParser)
set_promoter (Bio::Genscan::Report::Gene)
set_triangle (Bio::Nexus::DistancesBlock)
set_value (Bio::Nexus::NexusMatrix)
setup_colors (Bio::Shell::ColoredCodonTable)
setup_enzyme_and_reference_association (Bio::REBASE)
setup_enzyme_data (Bio::REBASE)
setup_irb (Bio::Shell::Irb)
setup_new_bin (Bio::RestrictionEnzyme::Range::SequenceRange)
setup_savedir (Bio::Shell::Setup)
sf (Bio::TRANSFAC::FACTOR)
sf (Bio::TRANSFAC::SITE)
sheet (Bio::PDB)
shell (Bio::Shell::Demo)
shell_dir (Bio::Shell::Core)
shift (Bio::Alignment::OriginalAlignment)
site (Bio::PROSITE)
size (Bio::Hinv::KeywordSearch)
size (Bio::Locations)
size (Bio::Alignment::OriginalAlignment)
size (Bio::FlatFileIndex::Results)
size (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
size (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
skip (String)
skip_flag (Bio::PROSITE)
skip_leader (Bio::Blast::Report::BlastXmlSplitter)
skip_leader (Bio::Blast::RPSBlast::RPSBlastSplitter)
skip_leader (Bio::FlatFile::Splitter::Template)
skip_leader (Bio::FlatFile::Splitter::Default)
skip_leader (Bio::Fasta::Report::FastaFormat10Splitter)
skip_leader (Bio::FlatFile::Splitter::LineOriented)
skip_spaces (Bio::FlatFile::BufferedInputStream)
slice (Bio::Alignment::EnumerableExtension)
small_world (Bio::Pathway)
so (Bio::MEDLINE)
so (Bio::TRANSFAC::SITE)
solexa_p2q (Bio::Sequence::QualityScore::Solexa)
solexa_q2p (Bio::Sequence::QualityScore::Solexa)
sort_attributes_by_tag! (Bio::GFF::GFF2::Record)
source (Bio::NCBIDB::Common)
source (Bio::MEDLINE)
sp_xref (Bio::PROSITE)
span (Bio::Locations)
speciations= (Bio::PhyloXML::Events)
species (Bio::EMBL)
species (Bio::SQL::Sequence)
species= (Bio::SQL::Sequence)
splash_message (Bio::Shell::Ghost)
splash_message_action (Bio::Shell::Ghost)
splash_message_action_color (Bio::Shell::Ghost)
splash_message_color (Bio::Shell::Ghost)
splice (Bio::Sequence::Common)
splicing (Bio::Sequence::Common)
split_label_value_in (Bio::SOFT)
sq (Bio::TRANSFAC::SITE)
sq (Bio::EMBL)
sq (Bio::TRANSFAC::FACTOR)
sq (Bio::SPTR)
ssbond (Bio::PDB)
st (Bio::TRANSFAC::SITE)
standard_comment? (Bio::Lasergene)
start (Bio::Fasta::Report::Hit::Query)
start (Bio::Hinv::KeywordSearch)
start_codon? (Bio::CodonTable)
start_http (Bio::Command)
start_irb (Bio::Shell::Irb)
statistics (Bio::KEGG::GENOME)
statistics (Bio::PROSITE)
statistics (Bio::Blast::Report)
status (Bio::Iprscan::Report::Match)
step (String)
sticky? (Bio::RestrictionEnzyme::DoubleStranded)
stop (Bio::Fasta::Report::Hit::Query)
stop_codon? (Bio::CodonTable)
store (Bio::Alignment::OriginalAlignment)
store (Bio::Shell::Web::Results)
store_history (Bio::Shell::Ghost)
str2scores (Bio::Fastq::FormatData)
strand (Bio::GenBank)
strand (Bio::Blat::Report::Hit)
strand (Bio::Spidey::Report::Hit)
strandedness (Bio::GenBank)
strands_for_display (Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts)
strip (Bio::Alignment::OriginalAlignment)
strip! (Bio::Alignment::EnumerableExtension)
strip_and_sort (Bio::RestrictionEnzyme::Fragments)
strip_cuts_and_padding (Bio::RestrictionEnzyme::StringFormatting)
strip_padding (Bio::RestrictionEnzyme::StringFormatting)
structure (Bio::KEGG::GENES)
structures (Bio::KEGG::ENZYME)
structures (Bio::KEGG::GENES)
subgraph (Bio::Pathway)
subseq (Bio::Sequence::Common)
subseq (Bio::Alignment::EnumerableExtension)
substrates (Bio::KEGG::ENZYME)
subtree (Bio::Tree)
subtree_with_all_paths (Bio::Tree)
sv (Bio::EMBL)
sw (Bio::Fasta::Report::Hit)
swissprot_release_number (Bio::PROSITE)
swissprot_release_sequences (Bio::PROSITE)
sy (Bio::TRANSFAC::FACTOR)
symbol_comparison_table (Bio::GCG::Msf)
symbols (Bio::PDB::Record)
synonyms (Bio::SPTR)
sysname (Bio::KEGG::ENZYME)
sz (Bio::TRANSFAC::FACTOR)
ta (Bio::MEDLINE)
tab (Bio::Blast::Report)
table_sum_all (Bio::ContingencyTable)
tags (Bio::DB)
target (Bio::Blat::Report::Hit)
target_avg (Bio::KEGG::EXPRESSION)
target_def (Bio::Fasta::Report::Hit)
target_def (Bio::HMMER::Report::Hit)
target_def (Bio::Spidey::Report::Hit)
target_def (Bio::Sim4::Report::Hit)
target_def (Bio::Blast::Default::Report::Hit)
target_def (Bio::Blat::Report::Hit)
target_end (Bio::Blast::Default::Report::Hit)
target_end (Bio::Fasta::Report::Hit)
target_end (Bio::Blast::Report::Hit)
target_from (Bio::HMMER::Report::Hsp)
target_id (Bio::Blast::Default::Report::Hit)
target_id (Bio::Fasta::Report::Hit)
target_id (Bio::Spidey::Report::Hit)
target_id (Bio::Blat::Report::Hit)
target_id (Bio::Sim4::Report::Hit)
target_len (Bio::Spidey::Report::Hit)
target_len (Bio::Blast::Default::Report::Hit)
target_len (Bio::Fasta::Report::Hit)
target_len (Bio::Sim4::Report::Hit)
target_len (Bio::Blat::Report::Hit)
target_sd (Bio::KEGG::EXPRESSION)
target_seq (Bio::Fasta::Report::Hit)
target_seq (Bio::Blast::Report::Hit)
target_seq (Bio::Blast::Default::Report::Hit)
target_seq (Bio::HMMER::Report::Hsp)
target_start (Bio::Blast::Default::Report::Hit)
target_start (Bio::Fasta::Report::Hit)
target_start (Bio::Blast::Report::Hit)
target_to (Bio::HMMER::Report::Hsp)
target_type (Bio::Fasta::Report::Hit)
target_var (Bio::KEGG::EXPRESSION)
taxa_list (Bio::KEGG::Keggtab)
taxid (Bio::KEGG::GENOME)
taxo2keggorgs (Bio::KEGG::Keggtab)
taxo2korgs (Bio::KEGG::Keggtab)
taxon2keggorgs (Bio::KEGG::Keggtab)
taxon2korgs (Bio::KEGG::Keggtab)
taxon_range (Bio::PROSITE)
taxonomy (Bio::SQL::Sequence)
taxonomy (Bio::NCBIDB::Common)
taxonomy (Bio::KEGG::GENOME)
taxonomy (Bio::KEGG::Keggtab)
taxonomy (Bio::NCBI::REST::EFetch::Methods)
termination_score (Bio::Genscan::Report::Exon)
three (Bio::AminoAcid::Data)
three2name (Bio::AminoAcid::Data)
three2one (Bio::AminoAcid::Data)
threshold (Bio::Fasta::Report)
ti (Bio::MEDLINE)
title (Bio::MEDLINE)
title (Bio::AAindex)
title (Bio::LITDB)
to= (Bio::PhyloXML::ProteinDomain)
to_1 (Bio::AminoAcid::Data)
to_3 (Bio::AminoAcid::Data)
to_a (Bio::MAFFT::Report)
to_a (Bio::FANTOM::MaXML::Sequences)
to_a (Bio::PDB::Record::ATOM)
to_a (Bio::GFF::GFF2::Record::Value)
to_a (Bio::FANTOM::MaXML::Annotations)
to_a (Bio::FlatFileIndex::Results)
to_a (Bio::FlatFile)
to_a (Bio::ClustalW::Report)
to_aaseq (String)
to_array_index (Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation)
to_array_index (Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation)
to_ary (Bio::PDB::Coordinate)
to_biosequence (Bio::EMBL)
to_biosequence (Bio::Fastq)
to_biosequence (Bio::SQL::Sequence)
to_biosequence (Bio::PhyloXML::Sequence)
to_biosequence (Bio::GenBank)
to_biosequence (Bio::FastaFormat)
to_biosequence (Bio::SangerChromatogram)
to_biosql (Bio::SQL::Sequence)
to_biotreenode (Bio::PhyloXML::Node)
to_clustal (Bio::Alignment::Output)
to_fasta (Bio::Alignment::OriginalAlignment)
to_fasta (Bio::ClustalW::Report)
to_fasta (Bio::MAFFT::Report)
to_fasta (Bio::SQL::Sequence)
to_fasta (Bio::Sequence::Common)
to_fasta_array (Bio::Alignment::OriginalAlignment)
to_fasta_reverse_complememt (Bio::SQL::Sequence)
to_fastaformat_array (Bio::Alignment::OriginalAlignment)
to_gcg (Bio::GCG::Seq)
to_hash (Bio::Iprscan::Report)
to_hash (Bio::Feature)
to_hash (Bio::Alignment::OriginalAlignment)
to_io (Bio::FlatFile::BufferedInputStream)
to_io (Bio::FlatFile)
to_list (Bio::Pathway)
to_matrix (Bio::Pathway)
to_midi (Bio::Sequence::NA)
to_naseq (String)
to_nbrf (Bio::NBRF)
to_nexus (Bio::Nexus::DataBlock)
to_nexus (Bio::Nexus::CharactersBlock)
to_nexus (Bio::Nexus::TreesBlock)
to_nexus (Bio::Nexus::TaxaBlock)
to_nexus (Bio::Nexus::GenericBlock)
to_nexus (Bio::Nexus::DistancesBlock)
to_nexus_helper (Bio::Nexus::Util)
to_nexus_row_array (Bio::Nexus::NexusMatrix)
to_re (Bio::NucleicAcid::Data)
to_re (Bio::Sequence::AA)
to_re (Bio::AminoAcid::Data)
to_re (Bio::Sequence::NA)
to_relations (Bio::Pathway)
to_s (Bio::GFF::GFF3::RecordBoundary)
to_s (Bio::FANTOM::MaXML)
to_s (Bio::FlatFileIndex::Flat_1::Record)
to_s (Bio::GFF::GFF2::Record)
to_s (Bio::PDB::Record::ATOM)
to_s (Bio::GFF::GFF2::MetaData)
to_s (Bio::FlatFileIndex::Results)
to_s (Bio::Blast::Default::Report)
to_s (Bio::GFF::GFF3)
to_s (Bio::GFF::GFF3::SequenceRegion)
to_s (Bio::FastaFormat)
to_s (Bio::GFF::GFF3::Record)
to_s (Bio::PDB)
to_s (Bio::GFF::GFF3::Record::Gap)
to_s (Bio::GFF::GFF3::Record::Gap::Code)
to_s (Bio::GFF::GFF3::Record::Target)
to_s (Bio::GFF::GFF2::Record::Value)
to_s (Bio::NBRF)
to_s (Bio::PDB::Chain)
to_s (Bio::PhyloXML::Date)
to_s (Bio::TMHMM::TMH)
to_s (Bio::FlatFileIndex::DataBank)
to_s (Bio::KEGG::Taxonomy)
to_s (Bio::Nexus::NexusMatrix)
to_s (Bio::FlatFileIndex::FileID)
to_s (Bio::PDB::Residue)
to_s (Bio::FlatFileIndex::NameSpaces)
to_s (Bio::Tree::Edge)
to_s (Bio::Tree::Node)
to_s (Bio::FastaDefline)
to_s (Bio::PDB::Model)
to_s (Bio::Nexus::GenericBlock)
to_s (Bio::Sequence::Common)
to_s (Bio::Nexus)
to_s (Bio::SQL::Location)
to_s (Bio::Sequence)
to_s (Bio::TMHMM::Report)
to_s (Bio::Locations)
to_s (Bio::GFF::GFF2)
to_seq (Bio::SangerChromatogram)
to_seq (Bio::FastaFormat)
to_str (Bio::Nexus::GenericBlock)
to_str (Bio::Sequence)
to_str (Bio::Sequence::Common)
to_str (Bio::Nexus)
to_str (Bio::GO::GeneAssociation)
to_str (Bio::GO::External2go)
to_str (Bio::Nexus::NexusMatrix)
to_string (Bio::FlatFileIndex::Flat_1::Record)
to_xml (Bio::PhyloXML::CladeRelation)
to_xml (Bio::PhyloXML::Events)
to_xml (Bio::PhyloXML::ProteinDomain)
to_xml (Bio::PhyloXML::SequenceRelation)
to_xml (Bio::PhyloXML::Other)
to_xml (Bio::PhyloXML::Accession)
to_xml (Bio::PhyloXML::Taxonomy)
to_xml (Bio::PhyloXML::Uri)
to_xml (Bio::PhyloXML::Confidence)
to_xml (Bio::PhyloXML::DomainArchitecture)
to_xml (Bio::PhyloXML::Polygon)
to_xml (Bio::PhyloXML::Annotation)
to_xml (Bio::PhyloXML::Sequence)
to_xml (Bio::PhyloXML::Id)
to_xml (Bio::PhyloXML::Property)
to_xml (Bio::PhyloXML::BranchColor)
to_xml (Bio::PhyloXML::Date)
to_xml (Bio::PhyloXML::BinaryCharacters)
to_xml (Bio::PhyloXML::Reference)
to_xml (Bio::PhyloXML::Distribution)
to_xml (Bio::PhyloXML::Node)
to_xml (Bio::PhyloXML::Point)
to_xyz (Bio::PDB::Utils)
too_short_parser (Bio::PSORT::PSORT2::Report)
topology (Bio::EMBL)
total (Bio::PROSITE)
total (Bio::Sequence::Common)
total_distance (Bio::Tree)
total_hits (Bio::PROSITE)
total_sequences (Bio::PROSITE)
tr (Bio::TRANSFAC::GENE)
translate (Bio::SQL::Seqfeature)
translate (Bio::Sequence::NA)
tree (Bio::Newick)
trends (Bio::Reference)
tsort_each_child (Bio::FlatFile::AutoDetect)
tsort_each_node (Bio::FlatFile::AutoDetect)
turn (Bio::PDB)
tutorial (Bio::Shell::Demo)
ty (Bio::TRANSFAC::SITE)
type= (Bio::PhyloXML::SequenceRelation)
type= (Bio::PhyloXML::Events)
ui (Bio::MEDLINE)
uitei (Bio::SiRNA)
uitei? (Bio::SiRNA)
undirected (Bio::Pathway)
undirected? (Bio::Pathway)
ungapped_pos (Bio::Alignment::GAP)
ungetc (Bio::FlatFile::BufferedInputStream)
ungets (Bio::FlatFile::BufferedInputStream)
unknown (Bio::PROSITE)
unknown_hits (Bio::PROSITE)
unknown_sequences (Bio::PROSITE)
unshift (Bio::Alignment::OriginalAlignment)
up_regulated (Bio::KEGG::EXPRESSION)
update_index (Bio::FlatFileIndex)
update_index (Bio::FlatFileIndex::Indexer)
v_parser (Bio::PSORT::PSORT2::Report)
val2rgb (Bio::KEGG::EXPRESSION)
validate_1 (Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair)
validate_2 (Bio::RestrictionEnzyme::DoubleStranded::CutLocationPairInEnzymeNotation)
validate_2 (Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair)
validate_args (Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation)
validate_args (Bio::RestrictionEnzyme::DoubleStranded::CutLocations)
validate_args (Bio::RestrictionEnzyme::SingleStrand)
validate_checksum (Bio::GCG::Seq)
validate_checksum (Bio::GCG::Msf)
validate_cut_locations (Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation)
validate_format (Bio::Fastq)
validate_input (Bio::RestrictionEnzyme::DoubleStranded::AlignedStrands)
value= (Bio::PhyloXML::Date)
values (Bio::Alignment::OriginalAlignment)
values (Bio::GFF::GFF2::Record::Value)
vernacular_name (Bio::NCBIDB::Common)
version (Bio::NCBIDB::Common)
version (Bio::PDB)
version (Bio::EMBL)
version (Bio::SQL::Sequence)
version (Bio::Blast::Default::Report)
version (Bio::DBGET)
version= (Bio::SQL::Sequence)
version_date (Bio::Blast::Default::Report)
version_number (Bio::Blast::Default::Report)
versions (Bio::NCBIDB::Common)
vertical_min_max_helper (Bio::RestrictionEnzyme::Range::CutRanges)
vi (Bio::MEDLINE)
volume (Bio::LITDB)
volume (Bio::MEDLINE)
warnings (Bio::Blast::WU::Report::Iteration)
warnings (Bio::Blast::WU::Report)
weight (Bio::AminoAcid::Data)
weight (Bio::NucleicAcid::Data)
width= (Bio::PhyloXML::Node)
window (Bio::Alignment::EnumerableExtension)
window_search (Bio::Sequence::Common)
with_cut_symbols (Bio::RestrictionEnzyme::SingleStrand)
with_spaces (Bio::RestrictionEnzyme::SingleStrand)
words (Bio::FastaDefline)
write (Bio::FlatFileIndex::DataBank)
write (Bio::PhyloXML::Writer)
write_other (Bio::PhyloXML::Writer)
write_record (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
writeback_array (Bio::FlatFileIndex::BDBwrapper)
wsdl= (Bio::SOAPWSDL)
x (Bio::PDB::Coordinate)
x= (Bio::PDB::Coordinate)
xmlparser (Bio::Blast::Report)
xyz (Bio::PDB::Coordinate)
xyz (Bio::PDB::Record::ATOM)
y (Bio::PDB::Coordinate)
y= (Bio::PDB::Coordinate)
year (Bio::MEDLINE)
z (Bio::PDB::Coordinate)
z= (Bio::PDB::Coordinate)