Documentation
Design Documentation
Coordinated OOP-Perl Modules for Biology
Getting Started
fetches sequences from bioperl indexed databases
indexes files for use by bpfetch
Modules
Handler for AlignIO Formats
bl2seq sequence input/output stream
clustalw sequence input/output stream
fasta sequence input/output stream
mase sequence input/output stream
msf sequence input/output stream
pfam sequence input/output stream
prodom sequence input/output stream
selex sequence input/output stream
stockholm sequence input/output stream
A generic object for annotations
A comment object, holding text
DESCRIPTION of Object
Specialised DBLink object for Literature References
Database object interface to ACeDB servers
Database object interface to GDB HTTP query
Database object interface to GenBank
Database object interface to GenPept
A collection of routines useful for queries to NCBI databases.
Abstract interface for a sequence database
Abstract Interface for Sequence databases
Database object interface to SwissProt retrieval
An interface for writing to a database of sequences.
Object Interface to generalize Web Databases for retrieving sequences
Abstract interface for any object wanting to use database cross references
Base class for factory classes loading drivers
class capable of creating SeqAnalysisParserI compliant parsers
interface describing objects capable of creating SeqAnalysisParserI compliant parsers
Abstract interface for indexing a flat file
Base class for AbstractSeq s
Interface for indexing (multiple) EMBL/Swissprot .dat files (ie flat file embl/swissprot format).
Interface for indexing (multiple) fasta files
Interface for indexing (multiple) GenBank .seq files (ie flat file GenBank format).
Interface for indexing swisspfam files
Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format).
AARange abstract class for LiveSeq
DoubleChain DataStructure for Perl
Double linked chain data structure
DNA object for LiveSeq
Range abstract class for LiveSeq
Range abstract class for LiveSeq
Loader for LiveSeq from EMBL entries with BioPerl
Parent Loader for LiveSeq
Loader for LiveSeq from EMBL entries with SRS
Range abstract class for LiveSeq
Mutation event descriptor class
Package mutating LiveSequences
Prim_Transcript class for LiveSeq
Range abstract class for LiveSeq
Repeat_Region class for LiveSeq
Repeat_Unit class for LiveSeq
Abstract sequence interface class for LiveSeq
Transcript class for LiveSeq
Translation class for LiveSeq
A Sequence object with start/end points on it
class implementing Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of a Location
Implementation of a Location on a Sequence which has unclear start and/or end locations
Abstract interface of a Location on a Sequence which has unclear start/end location
class implementing Bio::Location::CoordinatePolicy as the narrowest possible and reasonable range
Implementation of a Simple Location on a Sequence
Implementation of a Location on a Sequence which has multiple locations (start/end points)
Abstract interface of a Location on a Sequence which has multiple locations (start/end points)
class implementing Bio::Location::CoordinatePolicy as the widest possible and reasonable range
Abstract interface of a Location on a Sequence
Bioperl lightweight Sequence Object
Interface definition for a Bio::PrimarySeq
Pure perl RangeI implementation
Range interface
Exception class for Perl 5 objects
Global variables and utility functions
module providing several methods often needed when dealing with file IO
Input and output manager for Perl5 objects.
A core Perl 5 object.
Abstract interface to root object code
General-purpose utility module
Interface for managing linked lists of Perl5 objects.
A generic cross-reference object.
A perl wrapper around Sean Eddy's histogram object
Sequence object, with features
PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::RootI
SeqI compliant object that stores sequence as files in /tmp
Module implementing a sequence created from a rich sequence database entry
RichSeq interface, mainly for database orientated sequences
Sequence analysis output parser interface
hold pair feature information e.g. blast hits
a feature representing an exon
Interface for a feature representing an exon
A feature representing an arbitrarily complex structure of a gene
A feature representing an arbitrarily complex structure of a gene
A feature representing a transcript
Interface for a feature representing a transcript of exons, promoter(s), UTR, and a poly-adenylation site.
Generic SeqFeature
A sequence feature based on similarity
Sequence feature based on the similarity of two sequences.
Abstract interface of a Sequence Feature
Abstract Interface of Sequence (with features)
Handler for SeqIO Formats
Helper class for Embl/Genbank feature tables
Treating a set of files as a single input stream
ace sequence input/output stream
EMBL sequence input/output stream
fasta sequence input/output stream
Parses GAME XML 0.1 and higher into and out of Bio::Seq objects.
GCG sequence input/output stream
GenBank sequence input/output stream
method i/o on very large fasta sequence files
PIR sequence input/output stream
raw sequence file input/output stream
SCF sequence input/output stream
Swissprot sequence input/output stream
Additional methods for PrimarySeq objects
Multiple alignments held as a set of sequences
Generic species object
Base object for alignment factories
Base class for analysis result objects and parsers
Lightweight BLAST parser for pair-wise sequence alignment using the BLAST algorithm.
Lightweight BLAST parser
Bioperl BLAST sequence analysis object
Bioperl BLAST High-Scoring Segment Pair object
Bioperl Utility module for HTML formatting Blast reports
Bioperl module for running Blast analyses locally.
Bioperl module for running Blast analyses using a HTTP interface.
Bioperl BLAST "Hit" object
Bioperl codon table object
Results of one ESTScan run
Bioperl Fasta utility object
A Bio::SeqAnalysisParserI compliant GFF format parser
Results of one Genscan run
One particular domain hit from HMMER
Object representing HMMER output results
Set of identical domains from HMMER matches
Generates unique Seq objects from an ambiguous Seq object
Results of one MZEF run
Object holding alternative alphabet coding for one protein sequence
A predicted exon feature
a predicted gene structure feature
Bioperl object for a restriction endonuclease object.
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program
Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the TCoffee program
Object for the local execution of the NCBI Blast program suite (blastall, blastpgp, bl2seq)
Bioperl sequence analysis base class.
Bioperl object for a sequence pattern or motif
Object holding statistics for one particular sequence
Object holding n-mer statistics for one sequence
Bioperl object for sigcleave analysis
A single exon determined by an alignment
Results of one Sim4 run
Bioperl manager for web resources related to biology.
pairwise Smith Waterman object
Bioperl alignment object
Sequence change class for polypeptides
point mutation and codon information from single amino acid changes
Sequence object with allele-specific attributes
DNA level mutation class
Handler for sequence variation IO Formats
flat file sequence variation input/output stream
XML sequence variation input/output stream
Sequence change class for RNA level
Container class for mutation/variant descriptions
Sequence Change SeqFeature abstract class
Provides
in Bio/SeqIO/game/featureHandler.pm
in Bio/SeqIO/game/idHandler.pm
in Bio/SeqIO/game/seqHandler.pm
in Bio/Tools/BPlite/HSP.pm
in Bio/Tools/BPlite/Sbjct.pm
Examples
- examples/blast/blast_config.pl
- examples/blast/blast_seq.pl
- examples/blast/example.table1
- examples/blast/example.table2
- examples/blast/html.pl
- examples/blast/out/blastn.2.gz
- examples/blast/out/blastn.2.wu.gz
- examples/blast/out/blastp.1.gcg.gz
- examples/blast/out/blastp.1.gz
- examples/blast/out/blastp.2.gz
- examples/blast/out/blastp.2.nogap.gz
- examples/blast/out/blastp.2.wu
- examples/blast/out/blastp.205.gz
- examples/blast/out/blastp.2a.gz
- examples/blast/out/blastp.2b.gz
- examples/blast/out/blastp.email.html.gz
- examples/blast/out/blastx.2
- examples/blast/out/blastx.2.email.gz
- examples/blast/out/blastx.208.gz
- examples/blast/out/tblastn.206.out.gz
- examples/blast/parse_blast.pl
- examples/blast/parse_blast2.pl
- examples/blast/parse_multi.pl
- examples/blast/parse_positions.pl
- examples/blast/print_blasts.pl
- examples/blast/retrieve_blast.pl
- examples/blast/run_blast_remote.pl
- examples/blast/seq/acc1.dna.fasta
- examples/blast/seq/seqs.fasta
- examples/blast/seq/yal011w.dna.fasta
- examples/blast/seq/yel009c.fasta
- examples/blast/seq/ymr284w.fasta
- examples/blosum62.bla
- examples/change_gene.pl
- examples/clustalw.pl
- examples/getGenBank.pl
- examples/gon250.bla
- examples/gsequence
- examples/hitdisplay.pl
- examples/psw.pl
- examples/restriction.pl
- examples/rev_and_trans.pl
- examples/root_object/Bar.pm
- examples/root_object/Foo.pm
- examples/root_object/Outer.pm
- examples/root_object/destroy.pl
- examples/root_object/error.out
- examples/root_object/error.pl
- examples/root_object/filehandle.out
- examples/root_object/filehandle.pl
- examples/root_object/io.out
- examples/root_object/io.pl
- examples/root_object/read.pl
- examples/root_object/read.test
- examples/root_object/read.test2
- examples/root_object/read.test3
- examples/root_object/utilities.pl
- examples/root_object/vector/Person.pm
- examples/root_object/vector/PersonManager.pm
- examples/root_object/vector/vector.out
- examples/root_object/vector/vector.pl
- examples/seq/id.list
- examples/seq/seq.fasta.gz
- examples/seq/seq1.fasta
- examples/seq/seq2.fasta
- examples/seq/seqs1.pl
- examples/seq/seqs2.pl
- examples/seq/seqs3.pl
- examples/seq/seqtools.pl
- examples/seq_pattern.pl
- examples/simplealign.pl
- examples/standaloneblast.pl
- examples/test-genscan.pl