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The Journal of Supercomputing
Published in: The Journal of Supercomputing 3/2013

01-09-2013

Improving multiple sequence alignment biological accuracy through genetic algorithms

Authors: Miquel Orobitg, Fernando Cores, Fernando Guirado, Concepció Roig, Cedric Notredame

Published in: The Journal of Supercomputing | Issue 3/2013

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Abstract

Accuracy on multiple sequence alignments (MSA) is of great significance for such important biological applications as evolution and phylogenetic analysis, homology and domain structure prediction. In such analyses, alignment accuracy is crucial. In this paper, we investigate a combined scoring function capable of obtaining a good approximation to the biological quality of the alignment. The algorithm uses the information obtained by the different quality scores in order to improve the accuracy. The results show that the combined score is able to evaluate alignments better than the isolated scores.
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Literature
1.
Wang L, Jiang T (1994) On the complexity of multiple sequence alignment. J Comput Biol 4:337–348 CrossRef
2.
Notredame C (2007) Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol 3(8):e123 CrossRef
3.
Feng DF, Doolittle RF (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 4:351–360 CrossRef
4.
Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205–217 CrossRef
5.
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 CrossRef
6.
Notredame C, Higgins DG (1996) SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res 24(8):1515–1524 CrossRef
7.
Goldberg DE (1989) Genetic algorithms in search, optimisation, and machine learning. Addison-Wesley, Reading
8.
Edgar RC (2004) Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797 CrossRef
9.
10.
Lipman DJ, Altschul SF, Kececioglu JD (1989) A tool for multiple sequence alignment. Proc Natl Acad Sci USA 12(86):4412–4415 CrossRef
11.
Thompson JD, Plewniak F, Ripp R, Thierry JC, Poch O (2001) Towards a reliable objective function for multiple sequence alignments. J Mol Biol 4(314):937–951 CrossRef
12.
Kemena C, Taly JF, Kleinjung J, Notredame C (2011) STRIKE: evaluation of protein MSAs using a single 3D structure. Bioinformatics 24(27):3385–3391 CrossRef
13.
Notredame C, Holm L, Higgins DG (1998) COFFEE: an objective function for multiple sequence alignments. Bioinformatics 5(14):407–422 CrossRef
Metadata
Title
Improving multiple sequence alignment biological accuracy through genetic algorithms
Authors
Miquel Orobitg
Fernando Cores
Fernando Guirado
Concepció Roig
Cedric Notredame
Publication date
01-09-2013
Publisher
Springer US
Published in
The Journal of Supercomputing / Issue 3/2013
Print ISSN: 0920-8542
Electronic ISSN: 1573-0484
DOI
https://doi.org/10.1007/s11227-012-0856-9

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