match_seq
Martin Asser Hansen edited this page Oct 2, 2015
·
6 revisions
match_seq finds all matches between the first and the following sequences in the stream - or all self-self matches if only one sequence is found. This is useful for creating e.g. dotplots - see plot_matches.
match_seq requires MUMmer to be installed. Read more here:
http://mummer.sourceforge.net/
... | match_seq [options]
[-? | --help] # Print full usage description.
[-w <uint> | --word_size=<uint>] # Minimum match size - Default=20
[-d <string> | --direction=<string>] # Match direction: both|forward|reverse - Default=both
[-I <file!> | --stream_in=<file!>] # Read input from stream file - Default=STDIN
[-O <file> | --stream_out=<file>] # Write output to stream file - Default=STDOUT
[-v | --verbose] # Verbose output.
... | match_seq -w 25 -d forward
Martin Asser Hansen - Copyright (C) - All rights reserved.
August 2007
GNU General Public License version 2
http://www.gnu.org/copyleft/gpl.html
match_seq is part of the Biopieces framework.