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International Conference on Information Processing in Cells and Tissues

IPCAT 2012: Information Processign in Cells and Tissues pp 264–276Cite as

A Parallel Algorithm for Multiple Biological Sequence Alignment

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7223))

Abstract

The search of a multiple sequence alignment (MSA) is a well-known problem in bioinformatics that consists in finding a sequence alignment of three or more biological sequences. In this paper, we propose a parallel iterative algorithm for the global alignment of multiple biological sequences. In this algorithm, a number of processes work independently at the same time searching for the best MSA of a set of sequences. It uses a Longest Common Subsequence (LCS) technique in order to generate a first MSA. An iterative process improves the MSA by applying a number of operators that have been implemented to produce more accurate alignments. Simulations were made using sequences from the UniProKB protein database. A preliminary performance analysis and comparison with several common methods for MSA shows promising results. The implementation was developed on a cluster platform through the use of the standard Message Passing Interface (MPI) library.

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Author information

Authors and Affiliations

  1. Department of Information Systems, Universidad de Guadalajara, Periferico Norte 799-L308, Zapopan, Jal., Mexico, 45100

    Irma R. Andalon-Garcia, Arturo Chavoya & M. E. Meda-Campaña

Authors
  1. Irma R. Andalon-Garcia
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  2. Arturo Chavoya
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  3. M. E. Meda-Campaña
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Editor information

Editors and Affiliations

  1. Department of Electronics, University of York, YO10 5DD, York, UK

    Michael A. Lones  & Stephen L. Smith  & 

  2. MRC Laboratory of Molecular Biology, Hills Road, CB2 0QH, Cambridge, UK

    Sarah Teichmann

  3. The Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland

    Felix Naef

  4. Department of Electronics, University of York, YO10 5DD, York, UK

    James A. Walker  & Martin A. Trefzer  & 

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© 2012 Springer-Verlag Berlin Heidelberg

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Andalon-Garcia, I.R., Chavoya, A., Meda-Campaña, M.E. (2012). A Parallel Algorithm for Multiple Biological Sequence Alignment. In: Lones, M.A., Smith, S.L., Teichmann, S., Naef, F., Walker, J.A., Trefzer, M.A. (eds) Information Processign in Cells and Tissues. IPCAT 2012. Lecture Notes in Computer Science, vol 7223. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28792-3_31

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  • DOI: https://doi.org/10.1007/978-3-642-28792-3_31

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-28791-6

  • Online ISBN: 978-3-642-28792-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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