Search results for "Bio::SeqIO::embl"
Bio::SeqIO::embl - EMBL sequence input/output stream
This object can transform Bio::Seq objects to and from EMBL flat file databases. There is a lot of flexibility here about how to dump things which should be documented more fully. There should be a common object that this and Genbank share (probably ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::SeqIO - Handler for SeqIO Formats
- Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat file EMBL/Swissprot format).
- Bio::SeqIO::embldriver - EMBL sequence input/output stream
- 18 more results from BioPerl »
FAST::Bio::SeqIO::embl - EMBL sequence input/output stream
This object can transform FAST::Bio::Seq objects to and from EMBL flat file databases. There is a lot of flexibility here about how to dump things which should be documented more fully. There should be a common object that this and Genbank share (pro...
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
- 11 more results from FAST »
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
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::Panel - Generate GD images of Bio::Seq objects
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
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
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
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::Align::Subset - A BioPerl module to generate new alignments as subset from larger alignments
Given an array of codon positions and an alignment, the function Bio::Align::Subset->build_subset returns a new alignment with the codons at those positions from the original alignment....
HVALVERDE/Bio-Align-Subset-1.27 - 08 May 2013 17:33:42 UTC - Search in distribution
Bio::Variation::IO - Handler for sequence variation IO Formats
Bio::Variation::IO is a handler module for the formats in the Variation IO set (eg, Bio::Variation::IO::flat). It is the officially sanctioned way of getting at the format objects, which most people should use. The structure, conventions and most of ...
CJFIELDS/Bio-Variation-1.7.5 - 06 Jan 2020 19:59:16 UTC - Search in distribution
PerlIO::via::SeqIO - PerlIO layer for biological sequence formats
"PerlIO::via::SeqIO" attempts to provide an easy option for harnessing the magic sequence format I/O of the BioPerl (<http://bioperl.org>) toolkit. Opening a biological sequence file under "via(SeqIO)" yields a filehandle that can be used to read and...
MAJENSEN/PerlIO-via-SeqIO-0.0322 - 05 Dec 2009 20:28:53 UTC - Search in distribution