SW# - CUDA parallelized Smith Waterman with applying Hirschberg's algorithm Copyright (C) 2011 Matija Korpar

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Contact the author by [email protected].

1. DEPENDENCIES
2. INSTALLATION
3. USAGE

::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

1. DEPENDENCIES

Application uses following software:

1. Linux shell
2. gcc 4.*+
3. nvcc 2.*+
4. make

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 2) INSTALLATION ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

For installation run the install script in the application root directory from the command line. Application root directory must be writable.

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 3) USAGE ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

./sw# -i -j [OPTIONS] [FLAGS]

OPTIONS: --query, -i
fasta query file path --target, -j fasta database file path fasta database are appended fasta files in a single text file --matrix-file (optional) similarity matrix file path if given the similarity matrix is loaded from the file --matrix-table <BLOSUM50|BLOSUM55|BLOSUM62|BLOSUM70|DNA|BLAST|CHIAR> embedded similarity matrix (optional) (default: CHIAR) if given --matrix-file option won't be used --match (optional) match value
if --match and --mismatch are given, --matrix-table and --matrix-file options are not used --mismatch (optional) mismacth value
if --match and --mismatch are given, --matrix-table and --matrix-file options are not used --gap-open, -g (optional) (default: 5.0) gap open value --gap-extend, -e (optional) (default: 2.0) gap extend value
--threshold (optional) (default: NO_THRESHOLD) score threshold program will output not just the max score and its reconstruction, but all the scores which are above the given threshold --min-hits (optional) (default: 0) the option is used with --window option, it means there must be at least min_hits of matchings in every window length segment --window (optional) (default: 0) the option is used with --min-hits option, it means there must be at least min_hits of matchings in every window length segment FLAGS: --complement (optional) if input is a nucleotide, search also the other strand --solve (optional) solve only --cpu (optional) force CPU solving --param-search (optional) CUDA block and thread number optimization search --verbose (optional) verbose --global (optional) global aligment if given --threshold this option won't be used