parse
This program takes a BLAST output file and generates a report of matches. By default, HSPs with a score of 100 or greater are included in the report, though this can be changed with the '-c#' parameter. Matches that are adjacent are concatenated, and if '-s' is used, matches that are have a gap of 20 bp or less in both the query and target sequences are joined into a single match in the report.
Usage: parse [-b -c# -d -e# -f -g -ifilter.file -j -kPos_filter -l# -m -p -q -v -s] <blast.output >report
-b Color each database sequence which matches more than one place in the query sequence a unique color. Default is coloring according to BLAST score as the BLAST web server does.
-c# This option sets the HSP cutoff. HSPs of # or greater are included in the report. Default is 100.
-d Don't add a summary line to the fplot output. Ignored if -f (fplot output) is not set.
-e# If a number is given, the percent match considered a perfect match is set. By default, a perfect match is 98% or greater. If no number is given, printing of the perfect match summary list is turned off.
-f Generate output formatted for fplot.
-g Turn off output of multiple exon summary map.
-iFilter.file Use given filter file instead of the default, filter.parse.
-j Don't use any filter file.
-k[Pos_filter] Turn on positive filtering. The default positive filter file is 'keep.parse'. If positive filtering is turned on, only database sequences which match a entry in the positive filter file are retained. If a file name is given, that file will be used for positive filtering.
-l# This option allows the line length in the report to be changed.
-m Turn off output of the table which summarizes where along the query sequence matches are found.
-p Use % matching bp as a cutoff. All BLAST matches of less than the given % identical bp will be filtered out.
-q Print out this help information.
-v Use given pval cutoff instead of the default, .0001.
-s If this option is set, matches to a query sequence are concatenated when the gap between adjacent matches is less than 20 bp in both sequences. The gaps don't need to be identical in both query and target sequences, so shifts in one relative to the other are allowed.
Last updated 1/27/96
Written by Jim Lund in the lab of Roger Reeves, Johns Hopkins University