BP_NRDB(1p) User Contributed Perl Documentation BP_NRDB(1p)NAME
bp_nrdb.PLS - a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
bp_nrdb.PLS [options] file1 file2 file3
bp_nrdb.PLS -p [options] file1 id1 file2 id2 file3 id3
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
Jason Stajich, jason-at-bioperl-dot-org
perl v5.14.2 2012-03-02 BP_NRDB(1p)
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BP_SEARCH2TRIBE(1p) User Contributed Perl Documentation BP_SEARCH2TRIBE(1p)NAME
search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix
search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 ..
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 then feed the table into MCL
with the mcxdeblast script and the --m9 option.
This script will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering.
The options are:
-o filename - the output filename [default STDOUT]
-f format - search result format (blast, fasta)
(ssearch is fasta format). default is blast.
-w or --weight VALUE - Change the default weight for E(0.0) hits
to VALUE (default=200 (i.e. 1e-200) )
-h - this help menu
Additionally specify the filenames you want to process on the command-line. If no files are specified then STDIN input is assumed. You
specify this by doing: search2tribe < file1 file2 file3
Jason Stajich, jason-at-bioperl-dot-org
perl v5.14.2 2012-03-02 BP_SEARCH2TRIBE(1p)
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