Search results for "Bio::SeqIO::fasta"
Bio::SeqIO::fasta - fasta sequence input/output stream
This object can transform Bio::Seq objects to and from fasta flat file databases....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::SeqIO - Handler for SeqIO Formats
- Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
- Bio::Index::Qual - Interface for indexing (multiple) fasta qual files
- 36 more results from BioPerl »
FAST::Bio::SeqIO::fasta - fasta sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from fasta flat file databases....
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::SeqIO - Handler for SeqIO Formats
- FAST::Bio::Seq - Sequence object, with features
- FAST::Bio::Seq::SequenceTrace - Bioperl object packaging a sequence with its trace
- 17 more results from FAST »
lib/Bio/Gonzales/Seq/IO/Fasta.pm
JWB/Bio-Gonzales-0.083
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02 Jan 2021 23:10:48 UTC
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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::CUB::Calculator - A module to calculate codon usage bias (CUB) indice for protein-coding sequences
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::SeqHash - get one or more sequences from a FASTA file quickly.
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
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
Bioinfo::Fasta - get one or more sequences from a FASTA file quickly.
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 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
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 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
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
- 2 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::EMBL - Database object interface for EMBL entry retrieval
Allows the dynamic retrieval of sequence objects Bio::Seq from the EMBL database using the dbfetch script at EBI: <http://www.ebi.ac.uk/Tools/dbfetch/dbfetch>. In order to make changes transparent we have host type (currently only ebi) and location (...
CJFIELDS/Bio-DB-EMBL-1.7.4 - 04 Mar 2019 05:02:40 UTC - Search in distribution
CracTools::Utils - A set of useful functions
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/CracTools-1.251 - 09 Jun 2017 15:29:56 UTC - Search in distribution
Prospect::Align - Package for overlaying multiple Prospect alignments
Prospect::Align represents an alignment of one or more Prospect structural alignments....
REECE/Prospect-0.92 - 14 Nov 2003 13:16:46 UTC - Search in distribution- Prospect::Options - Package for representing options
- Prospect::LocalClient - execute Prospect locally $Id: LocalClient.pm,v 1.30 2003/11/07 18:42:42 cavs Exp $
- Prospect::SoapClient - execute Prospect remotely $Id: SoapClient.pm,v 1.11 2003/11/04 01:01:32 cavs Exp $
Bio::DB::RefSeq - Database object interface for RefSeq retrieval
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