Search results for "Bio::SeqIO"
Bio::SeqIO - Handler for SeqIO Formats
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::SeqIO::scf - .scf file input/output stream
- Bio::SeqIO::raw - raw sequence file input/output stream
- Bio::SeqIO::ace - ace sequence input/output stream
- 98 more results from BioPerl »
Bio::CUA::SeqIO - a package to parse sequence file if module Bio::SeqIO is unavailable in the system.
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- Bio::CUA::Seq - a module processing sequence object
- Bio::CUA::CUB::Calculator - A module to calculate codon usage bias (CUB) indice for protein-coding sequences
FAST::Bio::SeqIO - Handler for SeqIO Formats
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- FAST::Bio::SeqIO::pln - pln trace sequence input/output stream
- FAST::Bio::SeqIO::gcg - GCG sequence input/output stream
- FAST::Bio::SeqIO::abi - abi trace sequence input/output stream
- 85 more results from FAST »
Bio::SeqIO::nexml - NeXML sequence input/output stream
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
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
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- Bio::ASN1::EntrezGene::Indexer - Indexes NCBI Sequence files.
- Bio::ASN1::Sequence::Indexer - Indexes NCBI Sequence files.
Catalyst::View::Bio::SeqIO - use BioPerl's Bio::SeqIO as a Catalyst view
RBUELS/Catalyst-View-Bio-SeqIO-0.02
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21 Feb 2011 06:44:36 UTC
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Bio::Gonzales::Seq::IO - fast utility functions for sequence IO
JWB/Bio-Gonzales-0.083
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02 Jan 2021 23:10:48 UTC
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- lib/Bio/Gonzales/Seq/IO/Fasta.pm
- lib/Bio/Gonzales/Seq/IO/fastq.pm
- Bio::Gonzales::IDMapIO - remap ids of 'objects', should be used in IO-classes, like Bio::SeqIO
Bio::Graphics - Generate GD images of Bio::Seq objects
Please see Bio::Graphics::Panel for the full interface. Also try the script glyph_help.pl for quick help on glyphs and their options....
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC - Search in distribution- Bio::Graphics::Pictogram - generate SVG output of Pictogram display for consensus motifs
- Bio::Graphics::Panel - Generate GD images of Bio::Seq objects
- Bio::Graphics::FeatureFile - A set of Bio::Graphics features, stored in a file
- 1 more result from Bio-Graphics »
bioseq - Manipulation of FASTA sequences based on BioPerl
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...
YZHERNAND/Bio-BPWrapper-1.15 - 27 Feb 2024 16:55:31 UTC - Search in distribution
Mecom - A Perl module for protein contact interfaces evolutive analysis
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
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 distributionMCE::Shared - MCE extension for sharing data supporting threads and processes
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-1.886 - 13 Sep 2023 23:57:14 UTC - Search in distribution
Bio::ORA - Olfactory Receptor family Assigner (ORA) [bioperl module]
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::Perl - Functional access to BioPerl for people who don't know objects
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
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::Grep::Cookbook - Bio::Grep Cookbook
- Bio::Grep::Backend::RE - Perl Regular Expression back-end
- Bio::Grep::Backend::Vmatch - Vmatch back-end
- 4 more results from Bio-Grep »
Bio::DB::GFF - Storage and retrieval of sequence annotation data
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- Bio::DB::GFF::RelSegment - Sequence segment with relative coordinate support
Bio::Kmer - Helper module for Kmer Analysis.
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-0.5 - 08 Jan 2024 01:17:10 UTC - Search in distribution
Bio::Lite - Lightweight and fast module with a simplified API to ease scripting in bioinformatics
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
load_seqdatabase.pl
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::DB::BioDB - class creating the adaptor factory for a particular database
- Bio::DB::Query::QueryResultI - DESCRIPTION of Interface