Author:         Martin Asser Hansen - Copyright (C) - All rights reserved

Contact:        mail@maasha.dk

Date:           September 2007

License:        GNU General Public License version 2 (http://www.gnu.org/copyleft/gpl.html)

Description:    BLAST sequences in stream against a specified database.

Usage:          ... | blast_seq [options]

Options:   [-d <file>    | --database=<file>]        -  Path to database.
Options:   [-g <genome>  | --genome=<dm3|hg18|mm8>]  -  Choose genome instead of database.
Options:   [-p <program> | --program=<program>       -  blastn|blastp|tblastn|blastx|tblastx  -  Default=guessed!
Options:   [-e <float>   | --e_val=<float>]          -  Expectation value                     -  Default=10
Options:   [-f           | --filter]                 -  Filter low complexity sequence        -  Default=OFF
Options:   [-F           | --no_filter]              -  Disable low complexity filter         -  Default
Options:   [-c <int>     | --cpus=<int>]             -  Number of CPUs to use                 -  Default=1
Options:   [-I <file>    | --stream_in=<file>]       -  Read input from stream file           -  Default=STDIN
Options:   [-O <file>    | --stream_out=<file>]      -  Write output to stream file           -  Default=STDOUT

Examples:   ... | blast_seq -d my_database  -  BLAST sequences in stream against custom database.
Examples:   ... | blast_seq -g hg18         -  BLAST sequences in stream against hg18.