Bio::Seq - Sequence object, with features River stage two • 60 direct dependents • 65 total dependents

A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently Bio::Prim...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution

BioX::Seq - a (very) basic biological sequence object River stage one • 1 direct dependent • 1 total dependent

"BioX::Seq" is a simple sequence class that can be used to represent biological sequences. It was designed as a compromise between using simple strings and hashes to hold sequences and using the rather bloated objects of Bioperl. Features (or, depend...

VOLKENING/BioX-Seq-0.008002 - 21 Sep 2021 03:03:15 UTC - Search in distribution

BioUtil::Seq - Utilities for sequence River stage zero No dependents

SHENWEI/BioUtil-2015.0728 - 28 Jul 2015 02:07:44 UTC - Search in distribution

Bio::CUA::Seq - a module processing sequence object River stage zero No dependents

This module is called by Bio::CUA::SeqIO to create sequence object which has some basic methods required by the modules in the distribution <http://search.cpan.org/dist/Bio-CUA/>. The purpose of this module is to increase the portability of the distr...

FORTUNE/Bio-CUA-1.04 - 12 Jul 2015 19:52:07 UTC - Search in distribution

FAST::Bio::Seq - Sequence object, with features River stage zero No dependents

A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently FAST::Bio...

DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution

Bio::Gonzales::Seq - Gonzales Sequence Object River stage zero No dependents

JWB/Bio-Gonzales-0.083 - 02 Jan 2021 23:10:48 UTC - Search in distribution

Bio::MUST::Core::Seq - Nucleotide or protein sequence River stage one • 9 direct dependents • 9 total dependents

# TODO...

DBAURAIN/Bio-MUST-Core-0.212670 - 24 Sep 2021 14:29:46 UTC - Search in distribution

Bio::DB::Persistent::Seq - Proxy object for database PrimarySeq representations River stage zero No dependents

This is a proxy object which will ferry calls to/from database for the heavy stuff (sequence data) while it stores the simple attributes in memory. This object is obtained from a DBAdaptor....

CJFIELDS/BioPerl-DB-1.006900 - 15 Apr 2011 19:35:57 UTC - Search in distribution

Bio::BLAST::Database::Seq - lazy-loading sequence from a BLAST database River stage one • 1 direct dependent • 1 total dependent

Implements all methods in Bio::PrimarySeqI. Lazily loads its sequence information from the BLAST database it comes from, meaning that the sequence information is not actually loaded until you ask for it. Uses Bio::Seq::LargePrimarySeq internally when...

RBUELS/Bio-BLAST-0.4 - 12 Sep 2011 15:47:19 UTC - Search in distribution

lib/Bio/WGS2NCBI/Seq.pm River stage zero No dependents

RVOSA/Bio-WGS2NCBI-v0.1.2 - 23 Jan 2020 15:54:29 UTC - Search in distribution

Bio::Polloc::GroupCriteria::operator::seq - A sequence operator River stage zero No dependents

LRR/Polloc-1.5.3b - 29 Jun 2011 02:32:21 UTC - Search in distribution

Bio::DB::SoapEUtilities::FetchAdaptor::seq - Fetch adaptor for 'seq' efetch SOAP messages River stage one • 2 direct dependents • 2 total dependents

Returns an iterator over Bio::Seq or Bio::Seq::RichSeq objects, depending on the the return type of the "efetch". A standard "efetch" to a sequence database will return a GenBank SOAP result; this will be parsed into rich sequence objects: my $fac = ...

CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC - Search in distribution

Bio::SeqHash - get one or more sequences from a FASTA file quickly. River stage zero No dependents

Currently, there do have some modules that can operate the FASTA file such as Bio::SeqIO, But it only provide some basic operation to obtain the information about sequence. In my daily work, I still have to write some repetitive code. So this module ...

PEKINGSAM/Bio-SeqHash-0.1.4 - 24 Nov 2017 09:28:21 UTC - Search in distribution

Bio::SeqReader - Classes for reading sequence data. River stage zero No dependents

The Bio::SeqReader package provides classes specifically for reading sequence data. EXPORT None by default....

JAC/Bio-SeqReader-0.1.3 - 25 Sep 2012 04:13:30 UTC - Search in distribution

Bio::DB::USeq - Read USeq archive database files River stage zero No dependents

Bio::DB::USeq is a BioPerl style adaptor for reading USeq files. USeq files are compressed, indexed data files supporting modern bioinformatic datasets, including genomic points, scores, and intervals. More information about the USeq software package...

TJPARNELL/Bio-DB-USeq-0.25 - 02 Jan 2019 19:51:06 UTC - Search in distribution
  • USeqInfo.pl - A script to collect basic information about a USeq archive.

Bio::DB::RefSeq - Database object interface for RefSeq retrieval River stage one • 1 direct dependent • 8 total dependents

Allows the dynamic retrieval of sequence objects Bio::Seq from the RefSeq nucleotide database using the dbfetch script at EBI: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch At this time the module specifically retrieves nucleotide sequences only. In ord...

CJFIELDS/Bio-DB-RefSeq-1.7.4 - 07 Dec 2019 22:10:26 UTC - Search in distribution

Bio::SeqIO::nexml - NeXML sequence input/output stream River stage zero No dependents

This object can transform Bio::Seq objects to and from NeXML format. For more information on the NeXML standard, visit <http://www.nexml.org>....

CJFIELDS/Bio-NeXMLIO-1.7.3 - 11 Sep 2018 18:47:25 UTC - Search in distribution
  • Bio::NexmlIO - stream handler for NeXML documents
  • Bio::Nexml::Factory - A factory module for creating BioPerl and Bio::Phylo objects from/to nexml documents

Bio::SeqIO::excel - sequence input/output stream from a MSExcel-formatted table River stage zero No dependents

This class transforms records in a MS Excel workbook file into Bio::Seq objects. It is derived from the table format module and merely defines additional properties and overrides the way to get data from the file and advance to the next record. The m...

CJFIELDS/Bio-SeqIO-excel-1.7.3 - 25 Sep 2018 01:30:22 UTC - Search in distribution

Bio::DB::SeqFeature - Normalized feature for use with Bio::DB::SeqFeature::Store River stage zero No dependents

The Bio::DB::SeqFeature object is the default SeqFeature class stored in Bio::DB::SeqFeature databases. It implements both the Bio::DB::SeqFeature::NormalizedFeatureI and Bio::DB::SeqFeature::NormalizedTableFeatureI interfaces, which means that its s...

CJFIELDS/Bio-DB-SeqFeature-1.7.4 - 09 Jan 2020 04:03:49 UTC - Search in distribution

Bio::SeqIO::entrezgene - Entrez Gene ASN1 parser River stage two • 2 direct dependents • 12 total dependents

This is EntrezGene ASN bioperl parser. It is built on top of Bio::ASN1::EntrezGene, a low level ASN parser built by Mingyi Liu (<http://sourceforge.net/projects/egparser>). The easiest way to use it is shown above. You will get most of the Entrez Gen...

CJFIELDS/Bio-ASN1-EntrezGene-1.73 - 25 Sep 2018 02:32:11 UTC - Search in distribution
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