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bp_nrdb(1p) [debian man page]

BP_NRDB(1p)						User Contributed Perl Documentation					       BP_NRDB(1p)

bp_nrdb.PLS - a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases SYNOPSIS
Usage: bp_nrdb.PLS [options] file1 file2 file3 Alternative usage bp_nrdb.PLS -p [options] file1 id1 file2 id2 file3 id3 DESCRIPTION
This script will create a unique database of sequences (quasi-nonredundant). The options are: -o filename - the filename the db is written (STDOUT by default) -a filename - the filename to append the db to -l# - minimum required sequence length -i - do not check for duplicates -n# - max number of descriptions to report per seq -d# - delimiter to use between consecutive descriptions -p - use database id prefixes from command line AUTHOR
Jason Stajich, jason-at-bioperl-dot-org perl v5.14.2 2012-03-02 BP_NRDB(1p)

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BP_SEARCH2ALNBLOCKS(1p) 				User Contributed Perl Documentation				   BP_SEARCH2ALNBLOCKS(1p)

search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks SYNOPSIS
search2alnblocks --minid PERCENTID --minlen LEN --minevalue EVALUE file1. blast file2.blast ...> out.fas DESCRIPTION
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 be used to turn BLAST output into a FASTA alignment format for input into the QRNA comparative gene finder for RNA genes (E.Rivas). OPTIONS
--maxevalue Maximum E-value for an HSP --minevalue Minimum E-value for an HSP --minlen Minimum length of an HSP [default 0] --maxid Maximum Percent Id [default 100] (to help remove sequences which are really close) --minid Minimum Percent Identity for an HSP [default 0] -i/--input An optional input filename (expects input on STDIN by default) -o/--output An optional output filename (exports to STDOUT by default) -f/--format Specify a different Search Alignment format- {fasta, axt, waba, blast, blastxml} are all permitted although the format must have actual alignment sequence for this script to work See L<Bio::SearchIO> for more information. -of/--outformat Output format for the alignment blocks, anything L<Bio::AlignIO> supports. -v/--verbose Turn on debugging AUTHOR - Jason Stajich Jason Stajich, jason-at-bioperl-dot-org. perl v5.14.2 2012-03-02 BP_SEARCH2ALNBLOCKS(1p)
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