Search and SearchIO which are the principal Bioperl interfaces for Blast and FASTA report parsing, are described in this section. endobj Consequently the learning curve for actively developed, open source source software is sometimes steep. Consequently syntax for using LiveSeq objects is familiar although a modified version of SeqIO called Bio::LiveSeq::IO::Bioperl needs to be used to actually load the data, e.g. The Bio::Perl module provides some simple access functions, for example, this script will retrieve a swissprot sequence and write it out in fasta format. We recommend you use SearchIO, it's certain to be supported in future releases. This additional software includes perl modules from CPAN, package-libraries from bioperl's auxiliary code-repositories, a bioperl xs-extension, and several standard compiled bioinformatics programs. "�JE�p�j.s��A�(f%�p�QY�&�"�L�AC��'k�&6����p�bTI�M4�8Gu�� +hC�8�����)6]ԏ�u{��5�b�Aw�j.�8=\I�?��9)� �����xQ "����v��똀�@��Ll!b�N��|�~b�qhT�����(�x�?��K� Bioperl Tree objects can store data for all kinds of computer trees and are intended especially for phylogenetic trees. Brief introduction to bioperl's objects, II.1 Sequence objects (Seq, PrimarySeq, LocatableSeq, RelSegment, LiveSeq, LargeSeq, RichSeq, SeqWithQuality, SeqI), II.4 Interface objects and implementation objects, III.1 Accessing sequence data from local and remote databases, III.1.1 Accessing remote databases (Bio::DB::GenBank, etc), III.1.2 Indexing and accessing local databases (Bio::Index::*, bp_index.pl, bp_fetch.pl, Bio::DB::*), III.2 Transforming formats of database/ file records, III.2.1 Transforming sequence files (SeqIO), III.2.2 Transforming alignment files (AlignIO), III.3.1 Manipulating sequence data with Seq methods, III.3.2 Obtaining basic sequence statistics (SeqStats,SeqWord), III.3.3 Identifying restriction enzyme sites (Bio::Restriction), III.3.4 Identifying amino acid cleavage sites (Sigcleave), III.3.5 Miscellaneous sequence utilities: OddCodes, SeqPattern, III.3.6 Converting coordinate systems (Coordinate::Pair, RelSegment), III.4.1 Running BLAST (using RemoteBlast.pm), III.4.2 Parsing BLAST and FASTA reports with Search and SearchIO, III.4.3 Parsing BLAST reports with BPlite, BPpsilite, and BPbl2seq, III.4.4 Parsing HMM reports (HMMER::Results, SearchIO), III.4.5 Running BLAST locally (StandAloneBlast), III.5 Manipulating sequence alignments (SimpleAlign), III.6 Searching for genes and other structures on genomic DNA (Genscan, Sim4, Grail, Genemark, ESTScan, MZEF, EPCR), III.7 Developing machine readable sequence annotations, III.7.1 Representing sequence annotations (SeqFeature,RichSeq,Location), III.7.2 Representing sequence annotations (Annotation::Collection), III.7.3 Representing large sequences (LargeSeq), III.7.4 Representing changing sequences (LiveSeq), III.7.5 Representing related sequences - mutations, polymorphisms (Allele, SeqDiff), III.7.6 Incorporating quality data in sequence annotation (SeqWithQuality), III.7.7 Sequence XML representations - generation and parsing (SeqIO::game, SeqIO::bsml), III.7.8 Representing Sequences using GFF (Bio:DB:GFF ), III.8 Manipulating clusters of sequences (Cluster, ClusterIO), III.9 Representing non-sequence data in Bioperl: structures, trees and maps, III.9.1 Using 3D structure objects and reading PDB files (StructureI, Structure::IO), III.9.2 Tree objects and phylogenetic trees (Tree::Tree, TreeIO, PAML), III.9.3 Map objects for manipulating genetic maps (Map::MapI, MapIO), III.9.4 Bibliographic objects for querying bibliographic databases (Biblio), III.9.5 Graphics objects for representing sequence objects as images (Graphics), IV. <> Also see examples/bioperl.pl for more examples of usage of this module. Very large sequences present special problems to automated sequence-annotation storage and retrieval projects. Parsers for six widely used gene prediction programs - Genscan, Sim4, Genemark, Grail, ESTScan and MZEF - are available in bioperl. For example, if one wants to set up an indexed flat-file database of fasta files, and later wants then to retrieve one file, one could write scripts like: To facilitate the creation and use of more complex or flexible indexing systems, the bioperl distribution includes two sample scripts in the scripts/index directory, bp_index.PLS and bp_fetch.PLS. The labels won't change after insertions or deletions of the chain. A helper module CPAN.pm is available from CPAN which automates the process for installing the perl modules. : See Bio::LiveSeq::IO::BioPerl for more details. Bioperl includes a parser for converting between GFF files and SeqFeature objects. The standard perl distribution also contains a powerful interactive debugger with a command-line interface (use it like "perl -d