Search results for "Bio::SearchIO::blast"
Bio::SearchIO::blast - Event generator for event based parsing of blast reports
This object encapsulated the necessary methods for generating events suitable for building Bio::Search objects from a BLAST report file. Read the Bio::SearchIO for more information about how to use this. This driver can parse: * NCBI produced plain t...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::SearchIO::blast_pull - A parser for BLAST output
- Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
- Bio::Search::BlastUtils - Utility functions for Bio::Search:: BLAST objects
- 37 more results from BioPerl »
FAST::Bio::SearchIO::blast - Event generator for event based parsing of blast reports
This object encapsulated the necessary methods for generating events suitable for building FAST::Bio::Search objects from a BLAST report file. Read the FAST::Bio::SearchIO for more information about how to use this. This driver can parse: * NCBI prod...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::SearchIO::blast_pull - A parser for BLAST output
- FAST::Bio::SearchIO::XML::BlastHandler - XML Handler for NCBI Blast XML parsing.
- FAST::Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing.
- 28 more results from FAST »
Bio::Gonzales::Search::IO::BLAST
JWB/Bio-Gonzales-0.083
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02 Jan 2021 23:10:48 UTC
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Bio::SearchIO::XML::BlastHandler - XML Handler for NCBI Blast XML parsing.
This is the XML handler for BLAST XML parsing. Currently it passes elements off to the event handler, which is ultimately responsible for Bio::Search object generation. This was recently split off from the original code for Bio::SearchIO::blastxml pr...
CJFIELDS/Bio-SearchIO-blastxml-1.70 - 04 Jan 2018 02:12:33 UTC - Search in distribution- Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing.
- Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing.
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
search_overview - Render a SearchIO parser report into a simple overview graphic
This script will take any Bio::SearchIO parseable report and turn it into a simple overview graphic of the report. For our purposes we are assuming BLAST and the BLAST scores when assigning colors. Output is a PNG format file. This is not intended to...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC - Search in distribution- search_overview - Render a SearchIO parser report into a simple overview graphic
Bio::FastParsers - Classes for parsing bioinformatic programs output
This distribution includes modules for parsing the output files of a selection of sequence comparison programs, including BLAST <https://blast.ncbi.nlm.nih.gov/>, HMMER <http://hmmer.org/>, CD-HIT <https://github.com/weizhongli/cdhit> and UCLUST <htt...
DBAURAIN/Bio-FastParsers-0.221230 - 03 May 2022 21:00:40 UTC - Search in distribution
Bio::Tools::Run::TribeMCL
TribeMCL is a method for clustering proteins into related groups, which are termed 'protein families'. This clustering is achieved by analysing similarity patterns between proteins in a given dataset, and using these patterns to assign proteins into ...
CJFIELDS/BioPerl-Run-1.007003 - 08 Feb 2019 19:55:33 UTC - Search in distribution- Bio::Tools::Run::StandAloneBlast - Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). There is experimental support for WU-Blast and NCBI rpsblast.
- Bio::Tools::Run::StandAloneWUBlast - Object for the local execution of WU-Blast.
- Bio::Tools::Run::StandAloneNCBIBlast - Object for the local execution of the NCBI BLAST program suite (blastall, blastpgp, bl2seq). With experimental support for NCBI rpsblast.
- 1 more result from BioPerl-Run »
Bio::Tools::Run::RemoteBlast - Object for remote execution of the NCBI Blast via HTTP
Class for remote execution of the NCBI Blast via HTTP. For a description of the many CGI parameters see: https://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html Various additional options and input formats are available....
CJFIELDS/Bio-Tools-Run-RemoteBlast-1.7.3 - 25 Sep 2018 04:48:13 UTC - Search in distribution