MOSAL Multiobjective Sequence Alignment Tools

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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 860-410-0466 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 [7707407656]. 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 954-603-9190.


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 724-875-3962, 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