| |
bioperl.pod
(KO) |
생물학을 위한 객체지향 펄 모듈의 사용
|
| |
biostart.pod
(KO) |
Bioperl의 시작
|
| |
bptutorial.pl
(KO) |
Bioperl 매뉴얼 문서
|
| |
bioback.pod (KO)
|
Bioperl backend - 사용자에 따른
최적화 |
| |
Bio::AlignIO
(KO) |
AlignIO 형식의 조절
|
| |
Bio::Annotation
(KO) |
Annotations에 대한 일반 객체들
|
| |
Bio::DBLinkContainerI
(KO) |
데이터베이스 크로스 레퍼런스 사용을 원하는
객체에 대한 추상화 인터페이스 |
| |
Bio::LocatableSeq
(KO) |
시작과 종결을 갖는 서열 객체
|
| |
Bio::LocationI |
Abstract interface of a
Location on a Sequence |
| |
Bio::PrimarySeq |
Bioperl lightweight Sequence
Object |
| |
Bio::PrimarySeqI |
Interface definition for
a Bio::PrimarySeq |
| |
Bio::Range |
Pure perl RangeI implementation
|
| |
Bio::RangeI |
Range interface
|
| |
Bio::SearchDist |
A perl wrapper around Sean
Eddy's histogram object |
| |
Bio::SeqAnalysisParserI |
Sequence analysis output
parser interface |
| |
Bio::SeqFeatureI |
Abstract interface of a
Sequence Feature |
| |
Bio::Seq |
Sequence object, with features
|
| |
Bio::SeqI |
Abstract Interface of Sequence
|
| |
Bio::SeqIO |
Handler for SeqIO Formats
|
| |
Bio::SeqUtils |
Additional methods for PrimarySeq
objects |
| |
Bio::SimpleAlign |
Multiple alignments held
as a set of sequences |
| |
Bio::Species |
Generic species object
|
| |
Bio::UnivAln |
Bioperl alignment object
|
| |
Bio::AlignIO::bl2seq |
bl2seq sequence input/output
stream |
| |
Bio::AlignIO::clustalw |
clustalw sequence input/output
stream |
| |
Bio::AlignIO::fasta |
fasta sequence input/output
stream |
| |
Bio::AlignIO::mase |
mase sequence input/output
stream |
| |
Bio::AlignIO::msf |
msf sequence input/output
stream |
| |
Bio::AlignIO::pfam |
pfam sequence input/output
stream |
| |
Bio::AlignIO::prodom |
prodom sequence input/output
stream |
| |
Bio::AlignIO::selex |
selex sequence input/output
stream |
| |
Bio::AlignIO::stockholm |
stockholm sequence input/output
stream |
| |
Bio::Annotation::Comment |
A comment object, holding
text |
| |
Bio::Annotation::DBLink |
DESCRIPTION of Object
|
| |
Bio::Annotation::Reference |
Specialised DBLink object
for Literature References |
| |
Bio::DB::Ace |
Database object interface
to ACeDB servers |
| |
Bio::DB::GDB |
Database object interface
to GDB HTTP query |
| |
Bio::DB::GenBank |
Database object interface
to GenBank |
| |
Bio::DB::GenPept |
Database object interface
to GenPept |
| |
Bio::DB::NCBIHelper |
A collection of routines
useful for queries to NCBI databases |
| |
Bio::DB::RandomAccessI |
Abstract interface for a
sequence database |
| |
Bio::DB::SeqI |
Abstract Interface for Sequence
databases |
| |
Bio::DB::SwissProt |
Database object interface
to SwissProt retrieval |
| |
Bio::DB::UpdateableSeqI |
An interface for writing
to a database of sequences |
| |
Bio::DB::WebDBSeqI |
Object Interface to generalize
Web Databases for retrieving sequences |
| |
Bio::Factory::DriverFactory |
Base class for factory classes
loading drivers |
| |
Bio::Factory::SeqAnalysisParserFactory |
class capable of creating
SeqAnalysisParserI compliant parsers |
| |
Bio::Factory::SeqAnalysisParserFactoryI |
interface describing objects
capable of creating SeqAnalysisParserI compliant parsers
|
| |
Bio::Index::Abstract |
Abstract interface for indexing
a flat file |
| |
Bio::Index::AbstractSeq |
Base class for AbstractSeq
s |
| |
Bio::Index::EMBL |
Interface for indexing EMBL/Swissprot
dat files (ie flat file embl/swissprot format) |
| |
Bio::Index::Fasta |
Interface for indexing fasta
files |
| |
Bio::Index::GenBank |
Interface for indexing GenBank
seq files (ie flat file GenBank format) |
| |
Bio::Index::SwissPfam |
Interface for indexing swisspfam
files |
| |
Bio::Index::Swissprot |
Interface for indexing Swissprot
dat files (ie flat file swissprot format) |
| |
Bio::LiveSeq::AARange |
AARange abstract class for
LiveSeq |
| |
Bio::LiveSeq::Chain |
DoubleChain DataStructure
for Perl |
| |
Bio::LiveSeq::ChainI |
Double linked chain data
structure |
| |
Bio::LiveSeq::DNA |
DNA object for LiveSeq
|
| |
Bio::LiveSeq::Exon |
Range abstract class for
LiveSeq |
| |
Bio::LiveSeq::Gene |
Range abstract class for
LiveSeq |
| |
Bio::LiveSeq::Intron |
Range abstract class for
LiveSeq |
| |
Bio::LiveSeq::Mutation |
Mutation event descriptor
class |
| |
Bio::LiveSeq::Mutator |
Package mutating LiveSequences
|
| |
Bio::LiveSeq::Prim_Transcript |
Prim_Transcript class for
LiveSeq |
| |
Bio::LiveSeq::Range |
Range abstract class for
LiveSeq |
| |
Bio::LiveSeq::Repeat_Region |
Repeat_Region class for
LiveSeq |
| |
Bio::LiveSeq::Repeat_Unit |
Repeat_Unit class for LiveSeq
|
| |
Bio::LiveSeq::SeqI |
Abstract sequence interface
class for LiveSeq |
| |
Bio::LiveSeq::Transcript |
Transcript class for LiveSeq
|
| |
Bio::LiveSeq::Translation |
Translation class for LiveSeq
|
| |
Bio::LiveSeq::IO::BioPerl |
Loader for LiveSeq from
EMBL entries with BioPerl |
| |
Bio::LiveSeq::IO::Loader |
Parent Loader for LiveSeq
|
| |
Bio::LiveSeq::IO::SRS |
Loader for LiveSeq from
EMBL entries with SRS |
| |
Bio::Location::AvWithinCoordPolicy |
class implementing Bio::Location::CoordinatePolicy
as the average for WITHIN and the widest possible and reasonable range otherwise
|
| |
Bio::Location::CoordinatePolicyI |
Abstract interface for objects
implementing a certain policy of computing integer-valued coordinates of
a Location |
| |
Bio::Location::Fuzzy |
Implementation of a Location
on a Sequence which has unclear start and/or end locations
|
| |
Bio::Location::FuzzyLocationI |
Abstract interface of a
Location on a Sequence which has unclear start/end location
|
| |
Bio::Location::NarrowestCoordPolicy |
class implementing Bio::Location::CoordinatePolicy
as the narrowest possible and reasonable range |
| |
Bio::Location::Simple |
Implementation of a Simple
Location on a Sequence |
| |
Bio::Location::Split |
Implementation of a Location
on a Sequence which has multiple locations |
| |
Bio::Location::WidestCoordPolicy |
class implementing Bio::Location::CoordinatePolicy
as the widest possible and reasonable range |
| |
Bio::SplitLocationI |
Abstract interface of a
Location on a Sequence which has multiple locations |
| |
Bio::Root::Err |
Exception class for Perl
5 objects |
| |
Bio::Root::Global |
Global variables and utility
functions |
| |
Bio::Root::IO |
module providing several
methods often needed when dealing with file IO |
| |
Bio::Root::IOManager |
Input and output manager
for Perl5 objects |
| |
Bio::Root::Object |
Bioperl depreciated object
|
| |
Bio::Root::RootI |
Abstract interface to root
object code |
| |
Bio::Root::Utilities |
General-purpose utility
module |
| |
Bio::Root::Vector |
Interface for managing linked
lists of Perl5 objects |
| |
Bio::Root::Xref |
A generic cross-reference
object |
| |
Bio::Seq::LargePrimarySeq |
PrimarySeq object that stores
sequence as Bio::Root::RootI |
| |
Bio::Seq::LargeSeq |
SeqI compliant object that
stores sequence as files in /tmp |
| |
Bio::Seq::RichSeq |
Module implementing a sequence
created from a rich sequence database entry |
| |
Bio::Seq::RichSeqI |
RichSeq interface, mainly
for database orientated sequences |
| |
Bio::SeqFeature::FeaturePair |
hold pair feature information
eg blast hits |
| |
Bio::SeqFeature::Generic |
Generic SeqFeature
|
| |
Bio::SeqFeature::Similarity |
A sequence feature based
on similarity |
| |
Bio::SeqFeature::SimilarityPair |
Sequence feature based on
the similarity of two sequences |
| |
Bio::SeqFeature::Gene::Exon |
a feature representing an
exon |
| |
Bio::SeqFeature::Gene::ExonI |
Interface for a feature
representing an exon |
| |
Bio::SeqFeature::Gene::GeneStructure |
A feature representing an
arbitrarily complex structure of a gene |
| |
Bio::SeqFeature::Gene::GeneStructure |
A feature representing an
arbitrarily complex structure of a gene |
| |
Bio::SeqFeature::Gene::Transcript |
A feature representing a
transcript |
| |
Bio::SeqFeature::Gene::TranscriptI |
Interface for a feature
representing a transcript of exons, promoter, UTR, and a poly-adenylation
site |
| |
Bio::SeqIO::ace |
ace sequence input/output
stream |
| |
Bio::SeqIO::embl |
EMBL sequence input/output
stream |
| |
Bio::SeqIO::fasta |
fasta sequence input/output
stream |
| |
Bio::SeqIO::FTHelper |
Helper class for Embl/Genbank
feature tables |
| |
Bio::SeqIO::game |
Parses GAME XML 01 and higher
into and out of Bio::Seq objects |
| |
Bio::SeqIO::game::featureHandler |
** No documentation
yet |
| |
Bio::SeqIO::game::idHandler |
** No documentation
yet |
| |
Bio::SeqIO::game::seqHandler |
** No documentation
yet |
| |
Bio::SeqIO::gcg |
GCG sequence input/output
stream |
| |
Bio::SeqIO::GenBank |
GenBank sequence input/output
stream |
| |
Bio::SeqIO::largefasta |
method i/o on very large
fasta sequence files |
| |
Bio::SeqIO::MultiFile |
Treating a set of files
as a single input stream |
| |
Bio::SeqIO::pir |
PIR sequence input/output
stream |
| |
Bio::SeqIO::raw |
raw sequence file input/output
stream |
| |
Bio::SeqIO::scf |
SCF sequence input/output
stream |
| |
Bio::SeqIO::swiss |
Swissprot sequence input/output
stream |
| |
Bio::Tools::AlignFactory |
Base object for alignment
factories |
| |
Bio::Tools::AnalysisResult |
Base class for analysis
result objects and parsers |
| |
Bio::Tools::Blast |
Bioperl BLAST sequence analysis
object |
| |
Bio::Tools::BPbl2seq |
Lightweight BLAST parser
for pair-wise sequence alignment using the BLAST algorithm
|
| |
Bio::Tools::BPlite |
Lightweight BLAST parser
|
| |
Bio::Tools::BPpsilite |
Lightweight BLAST parser
for psiblast reports |
| |
Bio::Tools::CodonTable |
Bioperl codon table object
|
| |
Bio::Tools::ESTScan |
Results of one ESTScan run
|
| |
Bio::Tools::Fasta |
Bioperl Fasta utility object
|
| |
Bio::Tools::Genscan |
Results of one Genscan run
|
| |
Bio::Tools::GFF |
A Bio::SeqAnalysisParserI
compliant GFF format parser |
| |
Bio::Tools::IUPAC |
Generates unique Seq objects
from an ambiguous Seq object |
| |
Bio::Tools::MZEF |
Results of one MZEF run
|
| |
Bio::Tools::OddCodes |
Object holding alternative
alphabet coding for one protein sequence |
| |
Bio::Tools::pSW |
DESCRIPTION of Object
|
| |
Bio::Tools::RestrictionEnzyme |
Bioperl object for a restriction
endonuclease object |
| |
Bio::Tools::SeqAnal |
Bioperl sequence analysis
base class |
| |
Bio::Tools::SeqPattern |
Bioperl object for a sequence
pattern or motif |
| |
Bio::Tools::SeqStats |
Object holding statistics
for one particular sequence |
| |
Bio::Tools::SeqWords |
Object holding n-mer statistics
for one sequence |
| |
Bio::Tools::Sigcleave |
Bioperl object for sigcleave
analysis |
| |
Bio::Tools::WWW |
Bioperl manager for web
resources related to biology |
| |
Bio::Tools::Blast::HSP |
Bioperl BLAST High-Scoring
Segment Pair object |
| |
Bio::Tools::Blast::HTML |
Bioperl Utility module for
HTML formatting Blast reports |
| |
Bio::Tools::Blast::Sbjct |
Bioperl BLAST "Hit" object
|
| |
Bio::Tools::Blast::Run::LocalBlast |
Bioperl module for running
Blast analyses locally |
| |
Bio::Tools::Blast::Run::Webblast |
Bioperl module for running
Blast analyses using a HTTP interface |
| |
Bio::Tools::HMMER::Domain |
One particular domain hit
from HMMER |
| |
Bio::Tools::HMMER::Results |
Object representing HMMER
output results |
| |
Bio::Tools::HMMER::Set |
Set of identical domains
from HMMER matches |
| |
Bio::Tools::Prediction::Exon |
A predicted exon feature
|
| |
Bio::Tools::Prediction::Gene |
a predicted gene structure
feature |
| |
Bio::Variation::AAChange |
Sequence change class for
polypeptides |
| |
Bio::Variation::AAReverseMutate |
point mutation and codon
information from single amino acid changes |
| |
Bio::Variation::Allele |
Sequence object with allele-specific
attributes |
| |
Bio::Variation::DNAMutation |
DNA level mutation class
|
| |
Bio::Variation::IO |
Handler for sequence variation
IO Formats |
| |
Bio::Variation::RNAChange |
Sequence change class for
RNA level |
| |
Bio::Variation::SeqDiff |
Container class for mutation/variant
descriptions |
| |
Bio::Variation::VariantI |
Sequence Change SeqFeature abstract
class |