Bio::SeqIO - Handler for SeqIO Formats River stage two • 60 direct dependents • 65 total dependents

Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The Bio::SeqIO system can be thought of like biological file ...

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

Bio::CUA::SeqIO - a package to parse sequence file if module Bio::SeqIO is unavailable in the system. River stage zero No dependents

This is an auxiliary module to process sequences in case the module Bio::SeqIO is not installed in the system. At present, this module can only process fasta-formatted sequence file....

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

FAST::Bio::SeqIO - Handler for SeqIO Formats River stage zero No dependents

FAST::Bio::SeqIO is a handler module for the formats in the SeqIO set (eg, FAST::Bio::SeqIO::fasta). It is the officially sanctioned way of getting at the format objects, which most people should use. The FAST::Bio::SeqIO system can be thought of lik...

DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 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::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

Catalyst::View::Bio::SeqIO - use BioPerl's Bio::SeqIO as a Catalyst view River stage one • 1 direct dependent • 1 total dependent

RBUELS/Catalyst-View-Bio-SeqIO-0.02 - 21 Feb 2011 06:44:36 UTC - Search in distribution

bioseq - Manipulation of FASTA sequences based on BioPerl River stage zero No dependents

bioseq is a command-line utility for common, routine sequence manipulations based on BioPerl modules including Bio::Seq, Bio::SeqIO, Bio::SeqUtils, and Bio::Tools::SeqStats. By default, bioseq assumes that both the input and the output files are in F...

ROCKY/Bio-BPWrapper-1.13 - 02 Apr 2020 19:04:03 UTC - Search in distribution

Mecom - A Perl module for protein contact interfaces evolutive analysis River stage zero No dependents

This module integrates a workflow aimed to address the evolvability of the contact interfaces within a protein complex. The method "Mecom->run" launchs the whole analysis. Also, such workflow is divided into the following steps: Step 1, Structural an...

HVALVERDE/Mecom-1.15 - 13 Jul 2013 18:55:01 UTC - Search in distribution

AlignAid - easily run sequence alignments locally or on a cluster River stage zero No dependents

AlignAid is designed to make it easy to run the sequence alignment programs Blast and cross_match. AlignAid can accept a large number of query sequences. If a compute cluster queue such as LSF or PBS is available, AlignAid can automatically split the...

DMESSINA/AlignAid-v0.0.2 - 16 Dec 2006 01:04:35 UTC - Search in distribution

MCE::Shared - MCE extension for sharing data supporting threads and processes River stage one • 2 direct dependents • 3 total dependents

This module provides data sharing capabilities for MCE supporting threads and processes. MCE::Hobo provides threads-like parallelization for running code asynchronously....

MARIOROY/MCE-Shared-1.875 - 03 Dec 2021 11:51:54 UTC - Search in distribution

Bio::ORA - Olfactory Receptor family Assigner (ORA) [bioperl module] River stage zero No dependents

Bio::ORA is a featherweight object for identifying mammalian olfactory receptor genes. The sequences should not be longer than 40kb. The returned array include location, sequence and statistic for the putative olfactory receptor gene. Fully functiona...

CERATITES/ora-2.0 - 14 Jun 2016 15:58:05 UTC - Search in distribution

Bio::DB::GFF - Storage and retrieval of sequence annotation data River stage one • 2 direct dependents • 2 total dependents

Bio::DB::GFF provides fast indexed access to a sequence annotation database. It supports multiple database types (ACeDB, relational), and multiple schemas through a system of adaptors and aggregators. The following operations are supported by this mo...

CJFIELDS/Bio-DB-GFF-1.7.4 - 08 Jan 2020 20:41:58 UTC - Search in distribution

load_seqdatabase.pl River stage zero No dependents

This script loads a BioSQL database with sequences. There are a number of options that have to do with where the database is and how it's accessed and the format and namespace of the input files. These are followed by any number of file names. The fi...

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

Bio::Perl - Functional access to BioPerl for people who don't know objects River stage one • 6 direct dependents • 7 total dependents

Easy first time access to BioPerl via functions. read_sequence Title : read_sequence Usage : $seq = read_sequence('sequences.fa') $seq = read_sequence($filename,'genbank'); # pipes are fine $seq = read_sequence("my_fetching_program $id |",'fasta'); F...

CJFIELDS/Bio-Procedural-1.7.4 - 29 Nov 2019 20:57:49 UTC - Search in distribution

Bio::Grep - Perl extension for searching in DNA and Protein sequences River stage zero No dependents

Bio-Grep is a collection of Perl modules for searching in DNA and Protein sequences. It supports different back-ends, most importantly some (enhanced) suffix array implementations. Currently, there is no suffix array tool that works in all scenarios ...

LIMAONE/Bio-Grep-v0.10.6 - 12 Nov 2009 20:01:33 UTC - Search in distribution

Bio::Lite - Lightweight and fast module with a simplified API to ease scripting in bioinformatics River stage zero No dependents

Bio::Lite is a set of subroutines that aims to answer similar questions as Bio-perl distribution in a FAST and SIMPLE way. Bio::Lite does not make use of complexe data struture, or objects, that would lead to a slow execution. All methods can be impo...

JAUDOUX/Bio-Lite-0.003 - 23 Jul 2014 16:15:45 UTC - Search in distribution

Bio::Kmer - Helper module for Kmer Analysis. River stage one • 1 direct dependent • 1 total dependent

A module for helping with kmer analysis. The basic methods help count kmers and can produce a count of counts. Currently this module only supports fastq format. Although this module can count kmers with pure perl, it is recommended to give the option...

LSKATZ/Bio-Kmer-0.41 - 30 Aug 2020 16:32:34 UTC - Search in distribution

bp_pairwise_kaks - calculate pairwise Ka,Ks for a set of sequences River stage one • 1 direct dependent • 1 total dependent

This script will take as input a dataset of cDNA sequences, verify that they contain no stop codons, align them in protein space, project the alignment back into cDNA, and estimate the Ka (non-synonymous) and Ks (synonymous) substitutions based on th...

CDRAUG/Bio-Tools-Phylo-PAML-1.7.3 - 01 Jul 2018 12:36:38 UTC - Search in distribution

Bioinfo::Fasta - 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/Bioinfo-0.1.15 - 24 Sep 2019 02:44:11 UTC - Search in distribution
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