Search results for "Bio::SearchIO"
Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
This is a driver for instantiating a parser for report files from sequence database searches. This object serves as a wrapper for the format parsers in Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For people used...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::SearchIO::axt - a parser for axt format reports
- Bio::SearchIO::psl - A parser for PSL output (UCSC)
- Bio::SearchIO::sim4 - parser for Sim4 alignments
- 64 more results from BioPerl »
FAST::Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
This is a driver for instantiating a parser for report files from sequence database searches. This object serves as a wrapper for the format parsers in FAST::Bio::SearchIO::* - you should not need to ever use those format parsers directly. (For peopl...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::SearchIO::axt - a parser for axt format reports
- FAST::Bio::SearchIO::psl - A parser for PSL output (UCSC)
- FAST::Bio::SearchIO::sim4 - parser for Sim4 alignments
- 58 more results from FAST »
Bio::SearchIO::hmmer - A parser for HMMER2 and HMMER3 output (hmmscan, hmmsearch, hmmpfam)
This object implements a parser for HMMER output. It works with both HMMER2 and HMMER3...
CJFIELDS/Bio-SearchIO-hmmer-1.7.3 - 25 Sep 2018 00:26:52 UTC - Search in distribution- Bio::SearchIO::hmmer2 - A parser for HMMER output (hmmpfam, hmmsearch)
- Bio::SearchIO::hmmer3
- Bio::SearchIO::hmmer_pull - A parser for HMMER output
- 15 more results from Bio-SearchIO-hmmer »
Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing.
This object implements a NCBI Blast XML parser. It requires XML::SAX; it is also recommended (for faster parsing) that XML::SAX::ExpatXS or XML::LibXML be installed. Either 'XML::SAX::ExpatXS' or 'XML::LibXML::SAX::Parser' should be set as the defaul...
CJFIELDS/Bio-SearchIO-blastxml-1.70 - 04 Jan 2018 02:12:33 UTC - Search in distribution- Bio::SearchIO::XML::BlastHandler - XML Handler for NCBI Blast XML parsing.
- Bio::SearchIO::XML::PsiBlastHandler - XML Handler for NCBI Blast PSIBLAST XML parsing.
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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- lib/Bio/Gonzales/Search/IO/HMMER3.pm
- Bio::Gonzales::Domain::Identification::HMMER - Identify Protein Domains with HMMER
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
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
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
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::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
Bio::Tools::Run::ERPIN - Wrapper for local execution of the ERPIN suite of programs.
CJFIELDS/BioPerl-Run-1.007003
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08 Feb 2019 19:55:33 UTC
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- 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::StandAloneBlastPlus - Compute with NCBI's blast+ suite *ALPHA*
- Bio::Tools::Run::TribeMCL
- 7 more results from BioPerl-Run »