News
- Article "Heuristics for multiobjective multiple sequence alignment" accepted to Biomedical Engineering Online
- Conference article "Local Search for Multiobjective Multiple Sequence Alignment" accepted to IWBBIO2015
- Article "MOSAL: Software tools for multiobjective sequence alignment", accepted to Source Code for Biology and Medicine
- BiMuSA, an implementation for biobjective multiple sequence alignment problems, is available here (see technical report)
- Due to an unexpected hardware failure, the web server was down several times in the last two weeks. The problem is now fixed
- Online version of MOSAL is available here
- Poster accepted to the German Conference in Bionformatics 2013
Description
MOSAL is a program for computing the Pareto optimal alignments for the bicriteria pairwise sequence alignment. It allows the use of substitution matrices.
Support material for M.Abbasi, L. Paquete, A.Liefooghe, M. Pinheiro and P.Matias, Improvements on bicriteria pairwise sequence alignment: algorithms and applications, Bioinformatics, 29(8):996-1003, 2013.
Maintainer: Pedro Matias
License
This software is Copyright © 2013 M.Abbasi, L. Paquete, A.Liefooghe, M. Pinheiro and P.Matias.
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 2 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.
Appropriate reference to this software should be made when describing research in which it played a substantive role, so that it may be replicated and verified by others. The bicriteria sequence alignment problem and the algorithms which this software implements are described in detail in [1]. Please, mention the algorithm in the References section of your article. We would appreciate if you would email mosal@dei.uc.pt with citations of papers referencing this work. MOSAL is distributed under the GNU General Public License.
Download
Source code can be found here.
Try online
A limited version of the application is available online here.
Building
In GNU/Linux, the program can be compiled from source by invoking
$ make
Usage
$ ./mosal seq1_file seq2_file [gaps|indels] [dp|dpp -b=NUMBER] [-ss=FILE] [--no-traceback]
| Argument | Description |
|---|---|
seq1_file |
path to the 1st sequence file (FASTA format) |
seq1_file |
path to the 2nd sequence file (FASTA format) |
gaps |
use gaps |
indels |
use indels |
dp |
use Dynamic Programming |
dpp |
use Dynamic Programming with pruning (need to specify -b=NUMBER) |
-ss=FILE |
use substitution score(ss) instead of #matches (path to the ss table) |
-b=NUMBER |
specify the number of bounds for pruning version |
--no-traceback |
output only the scores without the alignments |
Output
- The non-traceback versions print only the score vectors. The first column corresponds to the number of matches/substitution scores and the second to the indels/gaps.
- The traceback versions print the scores and the corresponding alignments
References
| [1] | M.Abbasi, L. Paquete, A.Liefooghe, M. Pinheiro and P.Matias, Improvements on bicriteria pairwise sequence alignment: algorithms and applications, Bioinformatics, 29(8):996-1003, 2013. |
| [2] | L. Paquete, P. Matias, M. Abbasi, M. Pinheiro MOSAL: Software tools for multiobjective sequence alignment, Source Code for Biology and Medicine, 9(2), 2014. |
Acknowledgements
This work was support by the Fundação para a Ciência e Tecnologia, project MOSAL - Multiobjective sequence alignment (PTDC/EIA-CCO/098674/2008) and by FEDER, Programa Operacional Factores de Competitividade do QREN, ref. COMPETE: FCOMP-01-0124-FEDER-010024
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