match_seq

Biopiece: match_seq

Description

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/

Usage

... | match_seq [options]

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.

Examples

... | match_seq -w 25 -d forward

See also

plot_matches

Author

Martin Asser Hansen - Copyright (C) - All rights reserved.

[email protected]

August 2007

License

GNU General Public License version 2

http://www.gnu.org/copyleft/gpl.html

Help

match_seq is part of the Biopieces framework.

http://www.biopieces.org