S3 (Sequence Similarity Search) is a program for searching DNA or peptide sequences in protein database.
(1) Download the source code from Github
git clone git@github.com:acgtun/s3.git
(2) Build and Install
cd s3
make all
make install
makedb -d <protein database> -o <index file>
s3 -i <index file> -q <read files> -o <output file> [options]
| Option | Long Tag | Type | Default | Brief Description |
|---|---|---|---|---|
| -i | -index | String | NULL | index file created by makedb command ( .dbindex) |
| -q | -query | String | NULL | query file (.fastq or .fq) |
To see the list of options, use "-?" or "-help".
Haifeng Chen haifengc@usc.edu
Ting Chen tingchen@usc.edu
Copyright (C) 2016 University of Southern California
Authors: Haifeng Chen and Ting Chen
S3 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.
S3 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 S3. If not, see <http://www.gnu.org/licenses/>.