Methods

* (Bio::FlatFileIndex::Results)
+ (Bio::FlatFileIndex::Results)
+ (Bio::Sequence::Common)
<< (Bio::Sequence::Common)
<< (Bio::FlatFileIndex::Indexer::NameSpaces)
<< (Bio::Alignment::OriginalAlignment)
<=> (Bio::PDB::Chain)
<=> (Bio::PDB::Model)
<=> (Bio::PDB::Record::ATOM)
<=> (Bio::Map::Mapping)
<=> (Bio::PDB::Residue)
<=> (Bio::Location)
== (Bio::Alignment::OriginalAlignment)
== (Bio::FlatFileIndex::Flat_1::Record)
Pdb_LString (Bio::PDB::DataType::ConstLikeMethod)
Pdb_Real (Bio::PDB::DataType::ConstLikeMethod)
Pdb_String (Bio::PDB::DataType::ConstLikeMethod)
[] (Bio::CodonTable)
[] (Bio::FlatFileIndex::FileIDs)
[] (Bio::PDB::Residue)
[] (Bio::Feature)
[] (Bio::PDB::Model)
[] (Bio::NucleicAcid::Data)
[] (Bio::FlatFileIndex::BDBwrapper)
[] (Bio::Locations)
[] (Bio::FlatFile::AutoDetect)
[] (Bio::PDB::DataType::Pdb_LString)
[] (Bio::FlatFile::AutoDetect::RuleTemplate)
[] (Bio::CodonTable)
[] (Bio::PDB::DataType::Pdb_String)
[] (Bio::PDB)
[] (Bio::AAindex2)
[] (Bio::FastaNumericFormat)
[] (Bio::FANTOM::MaXML::Sequences)
[] (Bio::PDB::Chain)
[] (Bio::Alignment::OriginalAlignment)
[] (Bio::Features)
[] (Bio::FANTOM::MaXML::Annotations)
[] (Bio::PDB::Coordinate)
[] (Bio::AminoAcid::Data)
[] (Bio::PDB::DataType::Pdb_Real)
[]= (Bio::CodonTable)
[]= (Bio::Registry::DB)
[]= (Bio::FlatFileIndex::FileIDs)
[]= (Bio::FlatFileIndex::BDBwrapper)
__output_phylip_common (Bio::Alignment::Output)
__store__ (Bio::Alignment::OriginalAlignment)
aa (Bio::Sequence)
aa (Bio::AminoAcid::Data)
aalen (Bio::SPTR)
aalen (Bio::NBRF)
aalen (Bio::KEGG::GENES)
aalen (Bio::FastaFormat)
aalen (Bio::GenPept)
aaseq (Bio::NBRF)
aaseq (Bio::GCG::Seq)
aaseq (Bio::GenPept)
aaseq (Bio::SPTR)
aaseq (Bio::KEGG::GENES)
aaseq (Bio::FastaFormat)
aaseq (Bio::DBGET)
aaseq (Bio::PDB::Chain)
ab (Bio::MEDLINE)
absolute (Bio::Locations)
abstract (Bio::MEDLINE)
ac (Bio::TRANSFAC)
ac (Bio::EMBLDB::Common)
ac (Bio::PROSITE)
acc_version (Bio::FastaDefline)
acc_version (Bio::NCBIDB::Common)
acc_version (Bio::FastaFormat)
acceptor_score (Bio::Genscan::Report::Exon)
accession (Bio::FastaDefline)
accession (Bio::PDB)
accession (Bio::FastaFormat)
accession (Bio::NCBIDB::Common)
accession (Bio::EMBLDB::Common)
accession (Bio::Iprscan::Report::Match)
accessions (Bio::EMBLDB::Common)
accessions (Bio::FastaFormat)
accessions (Bio::NCBIDB::Common)
accessions (Bio::FastaDefline)
acos (Bio::PDB::Utils)
activity (Bio::KEGG::DRUG)
ad (Bio::MEDLINE)
add (Bio::FlatFileIndex::Indexer::NameSpaces)
add (Bio::FlatFileIndex::FileIDs)
add (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
add (Bio::FlatFile::AutoDetect)
addAtom (Bio::PDB::Residue)
addChain (Bio::PDB::Model)
addLigand (Bio::PDB::Chain)
addModel (Bio::PDB)
addResidue (Bio::PDB::Chain)
addSolvent (Bio::PDB::Model)
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_horizontal_cut_range (Bio::RestrictionEnzyme::Range::SequenceRange)
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_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::Spidey::Report::Hit)
align (Bio::MAFFT::Report)
align (Bio::ClustalW::Report)
align (Bio::Sim4::Report::Hit)
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::ClustalW::Report)
alignment (Bio::Alignment::MultiFastaFormat)
alignment (Bio::Phylip::PhylipFormat)
alignment (Bio::GCG::Msf)
alignment (Bio::MAFFT::Report)
alignment_collect (Bio::Alignment::OriginalAlignment)
alignment_collect (Bio::Alignment::HashExtension)
alignment_collect (Bio::Alignment::EnumerableExtension)
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)
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::Feature)
append (Bio::Pathway)
append (Bio::Features)
append (Bio::References)
append_hsp (Bio::HMMER::Report::Hit)
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)
au (Bio::MEDLINE)
author (Bio::AAindex)
author (Bio::LITDB)
authors (Bio::PDB)
authors (Bio::MEDLINE)
auto (Bio::Sequence)
auto (Bio::AAindex)
auto (Bio::FlatFile)
auto (Bio::Sequence)
autodetect (Bio::FlatFile::AutoDetect)
autodetect (Bio::FlatFile)
autodetect (Bio::FlatFile)
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::SITE)
bf (Bio::TRANSFAC::CLASS)
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::Fasta::Report::Hit)
bit_score (Bio::Blast::Default::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)
blunt? (Bio::RestrictionEnzyme::DoubleStranded)
bman (Bio::DBGET)
bootstrap= (Bio::Tree::Node)
bootstrap_string= (Bio::Tree::Node)
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)
cc (Bio::SPTR)
cc (Bio::TRANSFAC)
cc (Bio::PROSITE)
cc (Bio::EMBL)
cc_web_resource (Bio::SPTR)
cd (Bio::TRANSFAC::CELL)
cds_start (Bio::FANTOM::MaXML::Annotations)
cds_stop (Bio::FANTOM::MaXML::Annotations)
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_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::GenPept)
circular (Bio::GenBank)
cl (Bio::TRANSFAC::CLASS)
cl (Bio::TRANSFAC::FACTOR)
classes (Bio::KEGG::ENZYME)
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::FlatFile::BufferedInputStream)
close (Bio::FlatFileIndex::FileID)
close (Bio::FlatFileIndex::BDBwrapper)
close (Bio::FlatFileIndex::Template::NameSpace)
close (Bio::FlatFileIndex::DataBank)
close (Bio::FlatFileIndex::NameSpaces)
close (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
close (Bio::SQL)
close (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
close (Bio::FlatFile)
close (Bio::FlatFileIndex::FileIDs)
close (Bio::FlatFileIndex)
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::KEGG::GENES)
codon_usage (Bio::Sequence::NA)
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::GENOME)
comment (Bio::SQL::Sequence)
comment (Bio::PROSITE)
comment (Bio::KEGG::DRUG)
comment (Bio::KEGG::ENZYME)
comment (Bio::KEGG::GLYCAN)
comment (Bio::TRANSFAC)
comment (Bio::FastaFormat)
comment (Bio::KEGG::COMPOUND)
comment (Bio::AAindex)
comment (Bio::NCBIDB::Common)
comments (Bio::SQL::Sequence)
common_name (Bio::NCBIDB::Common)
common_name (Bio::SQL::Sequence)
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::RestrictionEnzyme::DoubleStranded::CutLocations)
complement (Bio::Sequence::NA)
complement (Bio::Location)
complement! (Bio::Sequence::NA)
complement? (Bio::Sim4::Report::Hit)
complement? (Bio::Spidey::Report::Hit)
complement_to_array_index (Bio::RestrictionEnzyme::DoubleStranded::CutLocationsInEnzymeNotation)
composition (Bio::Sequence::Common)
composition (Bio::KEGG::GLYCAN)
compounds (Bio::KEGG::GLYCAN)
concat (Bio::Sequence::Common)
concat (Bio::Tree)
concat (Bio::Alignment::OriginalAlignment)
conect (Bio::PDB::ChemicalComponent)
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::EnumerableExtension)
consensus_iupac (Bio::Alignment::SiteMethods)
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::Iteration)
converged? (Bio::Blast::Default::Report)
convert_match (Bio::Alignment::EnumerableExtension)
convert_to_xyz (Bio::PDB::Utils)
convert_unmatch (Bio::Alignment::EnumerableExtension)
copy (Bio::CodonTable)
correlation_coefficient (Bio::AAindex1)
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_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)
cut_symbol (Bio::RestrictionEnzyme::CutSymbol::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_dir (Bio::Shell::Core)
data_source (Bio::FANTOM::MaXML::Annotations)
data_source (Bio::KEGG::GENOME)
database (Bio::KEGG::Keggtab)
database (Bio::SQL::Sequence)
databases (Bio::Fetch)
datasrc (Bio::FANTOM::MaXML::Annotation)
date (Bio::TRANSFAC)
date (Bio::GenPept)
date (Bio::GenBank)
date (Bio::SQL::Sequence)
date (Bio::PROSITE)
date (Bio::Iprscan::Report::Match)
date (Bio::MEDLINE)
db (Bio::Blast::Default::Report)
db (Bio::Registry)
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)
dblink (Bio::SQL::Sequence)
dblinks (Bio::KEGG::GENES)
dblinks (Bio::KEGG::DRUG)
dblinks (Bio::AAindex)
dblinks (Bio::KEGG::GLYCAN)
dblinks (Bio::KEGG::COMPOUND)
dblinks (Bio::KEGG::ORTHOLOGY)
dblinks (Bio::KEGG::ENZYME)
dblinks_as_hash (Bio::KEGG::ORTHOLOGY)
dbref (Bio::PDB)
dbs (Bio::GO::External2go)
dbsource (Bio::GenPept)
de (Bio::EMBLDB::Common)
de (Bio::TRANSFAC::MATRIX)
de (Bio::PROSITE)
de (Bio::TRANSFAC::SITE)
de (Bio::TRANSFAC::GENE)
def_rec (Bio::PDB::Record)
default (Bio::FlatFile::AutoDetect)
default= (Bio::FlatFile::AutoDetect)
default_namespaces (Bio::FlatFileIndex)
default_namespaces= (Bio::FlatFileIndex)
default_parser (Bio::PSORT::PSORT1::Report)
default_parser (Bio::PSORT::PSORT2::Report)
definition (Bio::KEGG::ORTHOLOGY)
definition (Bio::KEGG::REACTION)
definition (Bio::SQL::Sequence)
definition (Bio::NCBIDB::Common)
definition (Bio::KEGG::GENES)
definition (Bio::Sim4::Report::Hit)
definition (Bio::KEGG::GENOME)
definition (Bio::Blast::Default::Report::Hit)
definition (Bio::AAindex)
definition (Bio::PDB)
definition (Bio::Blat::Report::Hit)
definition (Bio::Spidey::Report::Hit)
definition (Bio::EMBLDB::Common)
definition (Bio::PROSITE)
delete (Bio::Pathway)
delete (Bio::Alignment::OriginalAlignment)
depth_first_search (Bio::Pathway)
descendents (Bio::Tree)
description (Bio::FastaDefline)
description (Bio::Iprscan::Report::Match)
description (Bio::EMBLDB::Common)
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::Tree)
distance (Bio::PDB::Coordinate)
distance (Bio::PDB::Utils)
distance= (Bio::Tree::Edge)
distance_matrix (Bio::Tree)
distance_string= (Bio::Tree::Edge)
divent (Bio::PSORT::PSORT2::Report)
division (Bio::PROSITE)
division (Bio::KEGG::GENES)
division (Bio::EMBL)
division (Bio::GenBank)
division (Bio::GenPept)
dna (Bio::DAS)
dna (Bio::Sequence::NA)
dna! (Bio::Sequence::NA)
do_align (Bio::Alignment::OriginalAlignment)
do_index (bin/br_bioflat.rb)
do_parse (Bio::PDB::Record)
do_parse (Bio::PDB::Record::ATOM)
do_search (bin/br_bioflat.rb)
do_show_namespaces (bin/br_bioflat.rb)
doi (Bio::MEDLINE)
donor_score (Bio::Genscan::Report::Exon)
down_regulated (Bio::KEGG::EXPRESSION)
dp (Bio::MEDLINE)
dr (Bio::SPTR)
dr (Bio::TRANSFAC::FACTOR)
dr (Bio::TRANSFAC::SITE)
dr (Bio::PROSITE)
dr (Bio::TRANSFAC::CLASS)
dr (Bio::EMBLDB::Common)
dt (Bio::PROSITE)
dt (Bio::EMBL)
dt (Bio::SPTR)
dt (Bio::TRANSFAC)
dump_list (Bio::Pathway)
dump_matrix (Bio::Pathway)
dup (Bio::Alignment::OriginalAlignment)
each (Bio::FANTOM::MaXML::Sequences)
each (Bio::Blat::Report)
each (Bio::Fasta::Report)
each (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
each (Bio::FastaNumericFormat)
each (Bio::Sim4::Report)
each (Bio::PDB::Residue)
each (Bio::FlatFileIndex::Results)
each (Bio::Blast::Report)
each (Bio::Locations)
each (Bio::Sim4::Report::Hit)
each (Bio::Blast::Default::Report::Hit)
each (Bio::Blast::Default::Report::Iteration)
each (Bio::FlatFileIndex::FileIDs)
each (Bio::FlatFileIndex::Indexer::Parser::TemplateParser)
each (Bio::Alignment::OriginalAlignment)
each (Bio::PDB::Model)
each (Bio::Blat::Report::Hit)
each (Bio::Spidey::Report)
each (Bio::Feature)
each (Bio::Blast::Report::Iteration)
each (Bio::HMMER::Report::Hit)
each (Bio::PDB)
each (Bio::Blast::Report::Hit)
each (Bio::Features)
each (Bio::Spidey::Report::Hit)
each (Bio::FlatFile)
each (Bio::PDB::Chain)
each (Bio::Blast::Fastacmd)
each (Bio::FANTOM::MaXML::Annotations)
each (Bio::Blast::Default::Report)
each (Bio::REBASE)
each (Bio::CodonTable)
each (Bio::References)
each (Bio::HMMER::Report)
each (Bio::DAS::ENTRY_POINT)
each_atom (Bio::PDB::Residue)
each_atom (Bio::PDB::AtomFinder)
each_cds (Bio::EMBL)
each_cds (Bio::GenBank)
each_chain (Bio::PDB::Model)
each_chain (Bio::PDB::ChainFinder)
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::GenBank)
each_gene (Bio::EMBL)
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::Sim4::Report)
each_hit (Bio::Blat::Report)
each_hit (Bio::Blast::Report)
each_hit (Bio::Blast::Default::Report)
each_hsp (Bio::HMMER::Report::Hit)
each_iteration (Bio::Blast::Report)
each_iteration (Bio::Blast::Default::Report)
each_model (Bio::PDB)
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::ArrayExtension)
each_seq (Bio::Alignment::EnumerableExtension)
each_seq (Bio::Alignment::HashExtension)
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::Tree)
edges (Bio::Pathway)
efetch (Bio::PubMed)
efetch (Bio::PubMed)
eff_space (Bio::Blast::Report)
el (Bio::TRANSFAC::SITE)
elements (Bio::PDB::Coordinate)
elements (Bio::FlatFile::AutoDetect)
encode (Bio::Sequence::NA::MidiTrack)
endnote (Bio::Reference)
entret (Bio::EMBOSS)
entrez_query (Bio::Blast::Report)
entries (Bio::Alignment::MultiFastaFormat)
entropy (Bio::Blast::Default::Report)
entropy (Bio::Blast::Report)
entry (Bio::EMBL)
entry (Bio::KEGG::ENZYME)
entry (Bio::FastaFormat)
entry (Bio::NBRF)
entry (Bio::KEGG::GENES)
entry (Bio::SPTR)
entry (Bio::Shell::Demo)
entry_ended_pos (Bio::FlatFile)
entry_id (Bio::FANTOM::MaXML)
entry_id (Bio::AAindex)
entry_id (Bio::TRANSFAC)
entry_id (Bio::SPTR)
entry_id (Bio::FastaFormat)
entry_id (Bio::FANTOM::MaXML::Annotation)
entry_id (Bio::KEGG::GLYCAN)
entry_id (Bio::Fasta::Report::Hit::Query)
entry_id (Bio::MEDLINE)
entry_id (Bio::GenPept)
entry_id (Bio::KEGG::DRUG)
entry_id (Bio::Lasergene)
entry_id (Bio::GenBank)
entry_id (Bio::DB)
entry_id (Bio::KEGG::GENES)
entry_id (Bio::EMBL)
entry_id (Bio::PROSITE)
entry_id (Bio::KEGG::GENOME)
entry_id (Bio::PDB::ChemicalComponent)
entry_id (Bio::LITDB)
entry_id (Bio::TargetP::Report)
entry_id (Bio::KEGG::ORTHOLOGY)
entry_id (Bio::KEGG::COMPOUND)
entry_id (Bio::PDB)
entry_id (Bio::KEGG::REACTION)
entry_id (Bio::KEGG::ENZYME)
entry_name (Bio::SPTR)
entry_name (Bio::EMBL)
entry_pos_flag (Bio::FlatFile)
entry_pos_flag= (Bio::FlatFile)
entry_raw (Bio::FlatFile)
entry_start_pos (Bio::FlatFile)
enzyme_name? (Bio::REBASE)
enzyme_name? (Bio::RestrictionEnzyme)
enzymes (Bio::KEGG::COMPOUND)
enzymes (Bio::REBASE)
enzymes (Bio::KEGG::GLYCAN)
enzymes (Bio::KEGG::REACTION)
eof? (Bio::FlatFile::BufferedInputStream)
eof? (Bio::FlatFile)
equals? (Bio::Locations)
equation (Bio::KEGG::REACTION)
error_msg (Bio::SOFT)
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::PubMed)
esearch (Bio::PubMed)
evaluate (BiorubyController)
evalue (Bio::Fasta::Report::Hit)
evalue (Bio::Iprscan::Report::Match)
evalue (Bio::Blast::Report::Hit)
evalue (Bio::Blast::Default::Report::Hit)
events (Bio::Tree::Node)
evidence (Bio::FANTOM::MaXML::Annotations)
examples (PMFetch)
exec (Bio::Sim4)
exec (Bio::PTS1)
exec (Bio::PSORT::CGIDriver)
exec (Bio::PSORT::PSORT1)
exec (Bio::EMBOSS)
exec (Bio::PSORT::PSORT2)
exec_local (Bio::Sim4)
exists? (Bio::DB)
exon_type_long (Bio::Genscan::Report::Exon)
exons (Bio::Sim4::Report::Hit)
exons (Bio::Blat::Report::Hit)
exons (Bio::Spidey::Report::Hit)
expect (Bio::Blast::Report)
expect (Bio::Blast::WU::Report)
expected (Bio::ContingencyTable)
export_tsv (Bio::FlatFileIndex::Flat_1::FlatMappingFile)
exportview (Bio::Ensembl)
exportview (Bio::Ensembl::Base)
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_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)
features (Bio::NCBIDB::Common)
features (Bio::DAS)
features (Bio::EMBL)
features (Bio::SQL::Sequence)
fetch (Bio::DB)
fetch (Bio::Fetch)
fetch (Bio::SQL)
fetch (Bio::Blast::Fastacmd)
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::SecondaryNameSpace)
filename (Bio::FlatFileIndex::BDB_1::PrimaryNameSpace)
filename (Bio::FlatFileIndex::Template::NameSpace)
filename (Bio::FlatFileIndex::DataBank)
filename (Bio::FlatFileIndex::Flat_1::PrimaryNameSpace)
filename (Bio::FlatFileIndex::BDBwrapper)
filename (Bio::FlatFileIndex::Flat_1::SecondaryNameSpace)
filenames (Bio::FlatFileIndex::FileIDs)
fill (String)
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::FlatFile::BufferedInputStream)
foreach (Bio::FlatFile)
format (Bio::Reference)
format (Bio::FlatFileIndex::DataBank)
format= (Bio::Fasta)
format= (Bio::FlatFileIndex::DataBank)
format_embl (Bio::Sequence::Format)
format_fasta (Bio::Sequence::Format)
format_genbank (Bio::Sequence::Format)
format_raw (Bio::Iprscan::Report)
formats (Bio::Fetch)
formatstring2class (Bio::FlatFileIndex)
formul (Bio::PDB::ChemicalComponent)
formula (Bio::KEGG::DRUG)
formula (Bio::KEGG::COMPOUND)
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)
ft (Bio::EMBL)
ft (Bio::TRANSFAC::FACTOR)
ft (Bio::SPTR)
function (Bio::PTS1)
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::FANTOM::MaXML::Annotations)
gene_name (Bio::SPTR)
gene_names (Bio::SPTR)
general (Bio::Reference)
generate (Bio::Phylip::DistanceMatrix)
generate_colored_text (Bio::Shell::ColoredCodonTable)
generate_mono_text (Bio::Shell::ColoredCodonTable)
genes (Bio::KEGG::GENES)
genes (Bio::KEGG::ORTHOLOGY)
genes (Bio::KEGG::ENZYME)
genes_as_hash (Bio::KEGG::ORTHOLOGY)
genome_biol (Bio::Reference)
genome_res (Bio::Reference)
genomic (Bio::Spidey::Report::Hit)
geometricCentre (Bio::PDB::Utils)
get (Bio::DB)
get (Bio::FlatFileIndex::FileID)
get (Bio::FastaDefline)
get (Bio::FANTOM::MaXML::Sequences)
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_blocks (Bio::Nexus)
get_blocks_by_name (Bio::Nexus)
get_by_id (Bio::FlatFileIndex)
get_by_id (Bio::SQL)
get_by_id (Bio::Fetch)
get_by_id (Bio::FANTOM)
get_by_id (Bio::Blast::Fastacmd)
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::FlatFile::Splitter::Template)
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::NexusMatrix)
get_name (Bio::Nexus::GenericBlock)
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::DistancesBlock)
get_number_of_characters (Bio::Nexus::CharactersBlock)
get_number_of_taxa (Bio::Nexus::CharactersBlock)
get_number_of_taxa (Bio::Nexus::TaxaBlock)
get_number_of_taxa (Bio::Nexus::DistancesBlock)
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_sequence (Bio::Nexus::CharactersBlock)
get_sequence (Bio::DAS)
get_sequences_by_name (Bio::Nexus::CharactersBlock)
get_taxa (Bio::Nexus::TaxaBlock)
get_taxa (Bio::Nexus::DataBlock)
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::BufferedInputStream)
gets (Bio::FlatFile)
gi (Bio::NCBIDB::Common)
gi (Bio::FastaDefline)
gi (Bio::FastaFormat)
glycans (Bio::KEGG::COMPOUND)
gn (Bio::SPTR)
go_ids (Bio::GO::External2go)
go_terms (Bio::GO::External2go)
go_terms (Bio::Iprscan::Report::Match)
goid (Bio::GO::GeneAssociation)
goid2term (Bio::GO::Ontology)
gsub_entities (Bio::FANTOM::MaXML)
guess (Bio::FlatFile::AutoDetect::RuleProc)
guess (Bio::FlatFile::AutoDetect::RuleRegexp2)
guess (Bio::FlatFile::AutoDetect::RuleDebug)
guess (Bio::FlatFile::AutoDetect::RuleTemplate)
guess (Bio::Sequence)
guess (Bio::FlatFile::AutoDetect::RuleRegexp)
guess (Bio::Sequence)
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::Residue)
hetatm (Bio::PDB::Heterogen)
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)
hit_from (Bio::Sim4::Report::SegmentPair)
hit_from (Bio::Spidey::Report::SegmentPair)
hit_id (Bio::Spidey::Report::Hit)
hit_id (Bio::Sim4::Report::Hit)
hit_strand (Bio::Spidey::Report::SegmentPair)
hit_to (Bio::Sim4::Report::SegmentPair)
hit_to (Bio::Spidey::Report::SegmentPair)
hits (Bio::Blast::Default::Report)
hits (Bio::Blast::Report)
hits (Bio::Blast::Bl2seq::Report::Iteration)
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)
ho (Bio::TRANSFAC::FACTOR)
hoge (lib/bio/appl/targetp/report.rb)
hoge (lib/bio/appl/sosui/report.rb)
hseq (Bio::Sim4::Report::SegmentPair)
hseq (Bio::Spidey::Report::SegmentPair)
hsp_len (Bio::Blast::Report)
hsps (Bio::Spidey::Report::Hit)
hsps (Bio::Blat::Report::Hit)
hsps (Bio::Sim4::Report::Hit)
human (Bio::Ensembl)
iCode= (Bio::PDB::Residue)
icode (Bio::Sequence::NA::MidiTrack)
id_line (Bio::SPTR)
id_line (Bio::EMBL)
id_strings (Bio::FANTOM::MaXML::Sequence)
id_strings (Bio::FastaDefline)
id_strings (Bio::FANTOM::MaXML::Sequences)
identifiers (Bio::FastaFormat)
identity (Bio::Fasta::Report::Hit)
identity (Bio::Blast::Default::Report::Hit)
identity (Bio::Blast::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::RestrictionEnzyme::Range::CutRanges)
include? (Bio::RestrictionEnzyme::Range::HorizontalCutRange)
include? (Bio::Tree)
include? (Bio::FlatFileIndex::Template::NameSpace)
include? (Bio::FlatFileIndex)
include? (Bio::RestrictionEnzyme::Range::VerticalCutRange)
include_in_namespaces? (Bio::FlatFileIndex)
include_in_primary? (Bio::FlatFileIndex)
inclusion (Bio::Blast::Report)
index (Bio::AAindex1)
index (Bio::Alignment::OriginalAlignment)
index (BiorubyController)
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)
insert_node (Bio::Tree)
inspect (Bio::FlatFile::AutoDetect::RulesArray)
inspect (Bio::PDB::Chain)
inspect (Bio::Tree::Edge)
inspect (Bio::PDB::Residue)
inspect (Bio::PDB::Model)
inspect (Bio::PDB::Record)
inspect (Bio::FlatFile::AutoDetect)
inspect (Bio::Tree::Node)
inspect (Bio::PDB)
install_savedir (Bio::Shell::Setup)
interleaved? (Bio::Phylip::PhylipFormat)
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_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::MEDLINE)
journal (Bio::AAindex)
journal (Bio::LITDB)
jrnl (Bio::PDB)
kappa (Bio::Blast::Default::Report)
kappa (Bio::Blast::Report)
kcf (Bio::KEGG::GLYCAN)
kcf (Bio::KEGG::COMPOUND)
kcf (Bio::KEGG::DRUG)
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::BDBwrapper)
keys (Bio::FlatFileIndex::FileIDs)
keyword (Bio::LITDB)
keyword (Bio::SQL::Sequence)
keywords (Bio::NCBIDB::Common)
keywords (Bio::PDB)
keywords (Bio::EMBLDB::Common)
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::Default::Report::Hit)
lap_at (Bio::Blast::Report::Hit)
lap_over (Bio::Fasta::Report)
larger_than_zero (Bio::Nexus::Util)
last (Bio::Locations)
last (Bio::Features)
leaves (Bio::Tree)
left_padding (Bio::RestrictionEnzyme::StringFormatting)
len (Bio::Blast::Default::Report::Hit)
len (Bio::Spidey::Report::Hit)
len (Bio::Sim4::Report::Hit)
len (Bio::Blat::Report::Hit)
length (Bio::GenPept)
length (Bio::Fasta::Report::Hit::Query)
length (Bio::FastaFormat)
length (Bio::GenBank)
length (Bio::TargetP::Report)
length (Bio::Iprscan::Report::Match)
length (Bio::Locations)
length (Bio::FastaNumericFormat)
length (Bio::NBRF)
length (Bio::KEGG::GENOME)
library_id (Bio::FANTOM::MaXML::Sequence)
lineage (Bio::SQL::Sequence)
lineage (Bio::KEGG::GENOME)
list_classes (BiorubyController)
list_falsenegative (Bio::PROSITE)
list_falsepositive (Bio::PROSITE)
list_methods (BiorubyController)
list_methods (Bio::SOAPWSDL)
list_modules (BiorubyController)
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_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::GenBank)
locus (Bio::NCBIDB::Common)
locus (Bio::FastaFormat)
locus (Bio::FastaDefline)
locus (Bio::GenPept)
log (Bio::ClustalW)
log (Bio::Sim4)
log (Bio::MAFFT)
log= (Bio::SOAPWSDL)
logy_minus_logx (Bio::KEGG::EXPRESSION)
longer_than_zero (Bio::Nexus::Util)
lower_priority_elements (Bio::FlatFile::AutoDetect::RuleSpecial)
lowest_common_ancestor (Bio::Tree)
lstrip (Bio::Alignment::OriginalAlignment)
lstrip! (Bio::Alignment::EnumerableExtension)
ma (Bio::TRANSFAC::MATRIX)
ma (Bio::PROSITE)
ma2re (Bio::PROSITE)
make_cgi_params (Bio::Command)
make_cgi_params_key_value (Bio::Command)
make_command_line (Bio::Command)
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::BDB_1::PrimaryNameSpace)
mapping (Bio::FlatFileIndex::Template::NameSpace)
mapping (Bio::FlatFileIndex::Flat_1::PrimaryNameSpace)
mapping (Bio::FlatFileIndex::Flat_1::SecondaryNameSpace)
mappings_on (Bio::Map::ActsLikeMarker)
mass (Bio::KEGG::DRUG)
mass (Bio::KEGG::GLYCAN)
mass (Bio::KEGG::COMPOUND)
match (Bio::Blat::Report::Hit)
match_end (Bio::Iprscan::Report::Match)
match_line (Bio::ClustalW::Report)
match_line (Bio::Alignment::EnumerableExtension)
match_line_amino (Bio::Alignment::SiteMethods)
match_line_amino (Bio::Alignment::EnumerableExtension)
match_line_nuc (Bio::Alignment::SiteMethods)
match_line_nuc (Bio::Alignment::EnumerableExtension)
match_start (Bio::Iprscan::Report::Match)
matrix (Bio::Blast::Report)
matrix (Bio::AAindex2)
max (Bio::RestrictionEnzyme::Range::CutRanges)
max_repeat (Bio::PROSITE)
max_vertical (Bio::RestrictionEnzyme::Range::CutRanges)
maxids (Bio::Fetch)
merge (Bio::Alignment::OriginalAlignment)
merge! (Bio::Alignment::OriginalAlignment)
mesh (Bio::MEDLINE)
message (Bio::Blast::Report)
message (Bio::Blast::Default::Report)
method_missing (Bio::Iprscan::Report::Match)
method_missing (Bio::Registry::DB)
method_missing (Bio::NCBI::SOAP)
method_missing (Bio::KEGG::API)
method_missing (Bio::FastaDefline)
method_name (Bio::Iprscan::Report::Match)
mh (Bio::MEDLINE)
midline (Bio::Blast::Report::Hit)
midline (Bio::Blast::Default::Report::Hit)
milli_bad (Bio::Blat::Report::Hit)
min (Bio::RestrictionEnzyme::Range::CutRanges)
min_vertical (Bio::RestrictionEnzyme::Range::CutRanges)
mismatch (Bio::Blat::Report::Hit)
missing_char (Bio::Alignment::PropertyMethods)
missing_mrna_ends (Bio::Spidey::Report::Hit)
mito (Bio::Shell::Demo)
mm (Bio::TRANSFAC::SITE)
molecular_weight (Bio::Sequence::AA)
molecular_weight (Bio::Sequence::NA)
molecule (Bio::SPTR)
molecule (Bio::EMBL)
molecule_type (Bio::EMBL)
molecule_type (Bio::SPTR)
moltype (Bio::Fasta::Report::Hit::Query)
motif (Bio::KEGG::GENES)
motifs (Bio::KEGG::ENZYME)
mouse (Bio::Ensembl)
mrna (Bio::Spidey::Report::Hit)
mrna (Bio::Spidey::Report)
mx (Bio::TRANSFAC::FACTOR)
n_s (Bio::Blat::Report::Hit)
na (Bio::NucleicAcid::Data)
na (Bio::TRANSFAC::MATRIX)
na (Bio::Sequence)
nalen (Bio::NBRF)
nalen (Bio::GenBank)
nalen (Bio::KEGG::GENES)
nalen (Bio::FastaFormat)
nalen (Bio::KEGG::GENOME)
name (Bio::KEGG::ORTHOLOGY)
name (Bio::KEGG::ENZYME)
name (Bio::KEGG::COMPOUND)
name (Bio::KEGG::REACTION)
name (Bio::KEGG::Keggtab)
name (Bio::KEGG::GENES)
name (Bio::TargetP::Report)
name (Bio::KEGG::DRUG)
name (Bio::PROSITE)
name (Bio::AminoAcid::Data)
name (Bio::KEGG::GLYCAN)
name (Bio::KEGG::GENOME)
name (Bio::NucleicAcid::Data)
name2one (Bio::AminoAcid::Data)
name2three (Bio::AminoAcid::Data)
name= (Bio::FlatFile::AutoDetect::RuleSpecial)
name_by_abbrev (Bio::KEGG::Keggtab)
names (Bio::KEGG::DRUG)
names (Bio::Sequence::AA)
names (Bio::Sequence::NA)
names (Bio::KEGG::KGML::Entry)
names (Bio::KEGG::ORTHOLOGY)
names (Bio::KEGG::COMPOUND)
names (Bio::KEGG::ENZYME)
names (Bio::NucleicAcid::Data)
names (Bio::FlatFileIndex::NameSpaces)
names (Bio::FlatFileIndex::Indexer::NameSpaces)
names (Bio::AminoAcid::Data)
namespaces (Bio::FlatFileIndex)
nar (Bio::Reference)
naseq (Bio::KEGG::GENES)
naseq (Bio::GCG::Seq)
naseq (Bio::FastaFormat)
naseq (Bio::NBRF)
naseq (Bio::EMBL)
naseq (Bio::GenBank)
naseq (Bio::DBGET)
nature (Bio::Reference)
natype (Bio::GenBank)
ncbi_taxa_id (Bio::SQL::Sequence)
new (Bio::Blat::Report)
new (Bio::TRANSFAC::FACTOR)
new (Bio::Spidey::Report::Segment)
new (Bio::Spidey::Report::SegmentPair)
new (Bio::FlatFile::AutoDetect::RuleSpecial)
new (Bio::GenBank::Locus)
new (Bio::SOAPWSDL)
new (Bio::SQL)
new (Bio::TargetP::Report)
new (Bio::Location)
new (Bio::SOSUI::Report::TMH)
new (Bio::FastaDefline)
new (Bio::Spidey::Report)
new (Bio::LITDB)
new (Bio::Spidey::Report::Hit)
new (Bio::Sim4::Report::SeqDesc)
new (Bio::SOSUI::Report)
new (Bio::Ensembl)
new (Bio::HGC::HiGet)
new (Bio::Nexus::DataBlock)
new (Bio::Locations)
new (Bio::Sim4::Report::Hit)
new (Bio::DAS)
new (Bio::SiRNA::Pair)
new (Bio::PTS1::Report)
new (Bio::MAFFT::Report)
new (Bio::RestrictionEnzyme::DoubleStranded::CutLocations)
new (Bio::RestrictionEnzyme)
new (Bio::Blast)
new (Bio::SiRNA::ShRNA)
new (Bio::MEDLINE)
new (Bio::FlatFileIndex::Indexer::Parser)
new (Bio::Iprscan::Report)
new (Bio::FlatFileIndex::Indexer::Parser::GenPeptParser)
new (Bio::FlatFileIndex::Indexer::Parser::MaXMLClusterParser)
new (Bio::FlatFileIndex::Indexer::Parser::SPTRParser)
new (Bio::EMBLDB::Common)
new (Bio::EMBOSS)
new (Bio::Spidey::Report::SeqDesc)
new (Bio::Sim4::Report::SegmentPair)
new (Bio::References)
new (Bio::FlatFileIndex::BDB_1::BDBMappingFile)
new (Bio::Sim4::Report::Segment)
new (Bio::Lasergene)
new (Bio::PDB)
new (Bio::Sim4::Report)
new (Bio::EMBLDB)
new (Bio::Phylip::PhylipFormat)
new (Bio::FlatFileIndex::Indexer::Parser::GenBankParser)
new (Bio::Tree)
new (Bio::RestrictionEnzyme::DoubleStranded::CutLocationPair)
new (Bio::FlatFileIndex::Indexer::Parser::FastaFormatParser)
new (Bio::Nexus::NexusMatrix)
new (Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser)
new (Bio::FlatFile)
new (Bio::FlatFileIndex::Indexer::Parser::MaXMLSequenceParser)
new (Bio::FlatFileIndex::Indexer::Parser::TemplateParser)
new (Bio::Blat::Report::SegmentPair)
new (Bio::Reference)
new (Bio::RestrictionEnzyme::Range::HorizontalCutRange)
new (Bio::Newick)
new (Bio::Nexus::CharactersBlock)
new (Bio::FlatFileIndex::Indexer::Parser::BlastDefaultParser)
new (Bio::KEGG::ENZYME)
new (Bio::Alignment::FactoryTemplate::Simple)
new (Bio::FlatFileIndex::Indexer::Parser::EMBLParser)
new (Bio::Blat::Report::Hit)
new (Bio::RestrictionEnzyme::SingleStrand)
new (Bio::FlatFileIndex::Indexer::NameSpaces)
new (Bio::Sim4)
new (Bio::DDBJ::XML)
new (Bio::RestrictionEnzyme::Range::SequenceRange)
new (Bio::ContingencyTable)
new (Bio::FlatFileIndex::Indexer::NameSpace)
new (Bio::Pathway)
new (Bio::Alignment::MultiFastaFormat)
new (Bio::SiRNA)
<