Search results for "Bio::SearchIO::fasta"
Bio::SearchIO::fasta - A SearchIO parser for FASTA results
This object contains the event based parsing code for FASTA format reports. It creates Bio::Search::HSP::FastaHSP objects instead of Bio::Search::HSP::GenericHSP for the HSP objects. This module will parse -m 9 -d 0 output as well as default m 1 outp...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC - Search in distribution- Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
- Bio::AlignIO::fasta - fasta MSA Sequence input/output stream
- bp_search2gff - turn a SearchIO report into GFF
- 16 more results from BioPerl »
FAST::Bio::SearchIO::fasta - A SearchIO parser for FASTA results
This object contains the event based parsing code for FASTA format reports. It creates FAST::Bio::Search::HSP::FastaHSP objects instead of FAST::Bio::Search::HSP::GenericHSP for the HSP objects. This module will parse -m 9 -d 0 output as well as defa...
DHARD/FAST-1.06 - 21 Apr 2015 08:04:25 UTC - Search in distribution- FAST::Bio::SearchIO - Driver for parsing Sequence Database Searches (BLAST, FASTA, ...)
- FAST::Bio::Search::Hit::HitI - Interface for a hit in a similarity search result
- FAST::Bio::Search::HSP::GenericHSP - A "Generic" implementation of a High Scoring Pair
- 9 more results from FAST »
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::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::Hmmer - Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch
Wrapper module for Sean Eddy's HMMER suite of program to allow running of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam and hmmsearch. Binaries are available at http://hmmer.janelia.org/ You can pass most options understood by the command-line p...
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::StandAloneBlastPlus - Compute with NCBI's blast+ suite *ALPHA*
- Bio::Tools::Run::Alignment::Exonerate