Search results for "dist:BioPerl blast search"
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
Bio::Search::BlastUtils - Utility functions for Bio::Search:: BLAST objects
The BlastUtils.pm module is a collection of subroutines used primarily by Bio::Search::Hit::BlastHit objects for some of the additional functionality, such as HSP tiling. Right now, the BlastUtils is just a collection of methods, not an object, and i...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::BlastHit - Blast-specific subclass of Bio::Search::Hit::GenericHit
This object is a subclass of Bio::Search::Hit::GenericHit and provides some operations that facilitate working with BLAST and PSI-BLAST Hits. For general information about working with Hits, see Bio::Search::Hit::GenericHit....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::BlastHSP - Bioperl BLAST High-Scoring Pair object
A Bio::Search::HSP::BlastHSP object provides an interface to data obtained in a single alignment section of a Blast report (known as a "High-scoring Segment Pair"). This is essentially a pairwise alignment with score information. BlastHSP objects are...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::BlastStatistics - An object for Blast statistics
This is a basic container to hold the statistics returned from a Blast....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Result::BlastResult - Blast-specific subclass of Bio::Search::Result::GenericResult
This object is a subclass of Bio::Search::Result::GenericResult and provides some operations that facilitate working with BLAST and PSI-BLAST results. For general information about working with Results, see Bio::Search::Result::GenericResult....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::PsiBlastHit - Bioperl BLAST Hit object
The Bio::Search::Hit::PsiBlastHit.pm module encapsulates data and methods for manipulating "hits" from a BLAST report. A BLAST hit is a collection of HSPs along with other metadata such as sequence name and score information. Hit objects are accessed...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::PsiBlastHSP - Bioperl BLAST High-Scoring Pair object
A Bio::Search::HSP::PsiBlastHSP object provides an interface to data obtained in a single alignment section of a Blast report (known as a "High-scoring Segment Pair"). This is essentially a pairwise alignment with score information. PsiBlastHSP objec...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::BlastPullHit - A parser and hit object for BLASTN hits
This object implements a parser for BLASTN hit output....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::HSP::BlastPullHSP - A parser and HSP object for BlastN hsps
This object implements a parser for BlastN hsp output....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Result::BlastPullResult - A parser and result object for BLASTN results
This object implements a parser for NCBI BLASTN result output....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SearchIO::blast_pull - A parser for BLAST output
This object implements a pull-parser for BLAST output. It is fast since it only does work on request (hence 'pull'). Currently only NCBI BLASTN and BLASTP are supported....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
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
bp_search2gff - turn a SearchIO report into GFF
This script will turn a SearchIO report (BLAST, FASTP, SSEARCH, AXT, WABA) into GFF. The options are: -i infilename - (optional) inputfilename, will read either ARGV files or from STDIN -o filename - the output filename [default STDOUT] -f format - s...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix
This script is probably too slow for most people's uses. It is better to use something like scripts/searchio/fastam9_to_table, -m 9 output from BLAST, or the blast2table from the BLAST O'Reilly book to get a tabular output from these programs and the...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::Lucy - Object for analyzing the output from Lucy, a vector and quality trimming program from TIGR
Bio::Tools::Lucy.pm provides methods for analyzing the sequence and quality values generated by Lucy program from TIGR. Lucy will identify vector, poly-A/T tails, and poor quality regions in a sequence. (www.genomics.purdue.edu/gcg/other/lucy.pdf) Th...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_mask_by_search - mask sequence(s) based on its alignment results
Mask sequence based on significant alignments of another sequence. You need to provide the report file and the entire sequence data which you want to mask. By default this will assume you have done a TBLASTN (or TFASTY) and try and mask the hit seque...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
bp_search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks
This script will parse and filter BLAST (or other formats Bio::SearchIO can parse) output and format the alignment as blocks of alignments based on the HSPs. Note this can only work if the input file parsed contains the necessary. Typically this can ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::HitI - Interface for a hit in a similarity search result
Bio::Search::Hit::* objects are data structures that contain information about specific hits obtained during a library search. Some information will be algorithm-specific, but others will be generally defined....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AnalysisParserI - Generic analysis output parser interface
AnalysisParserI is a interface for describing generic analysis result parsers. This module makes no assumption about the nature of analysis being parsed, only that zero or more result sets can be obtained from the input source. This module was derive...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC