GapsMis: flexible sequence alignment with a bounded number of gaps

  • Authors:

  • Carl Barton;Tomáš Flouri;Costas S. Iliopoulos;Solon P. Pissis

  • Affiliations:

  • King's College London, Dept. of Informatics, United Kingdom;Heidelberg Institute for Theoretical Studies, Germany;King's College London, Dept. of Informatics, United Kingdom;Florida Museum of Natural History, University of Florida, USA

  • Venue:
  • Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
  • Year:
  • 2013

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Abstract

Motivation: Recent developments in next-generation sequencing technologies have renewed interest in pairwise sequence alignment techniques, particularly so for the application of re-sequencing---the assembly of a genome directed by a reference sequence. After the fast alignment between a factor of the reference sequence and the high-quality fragment of a short read, an important problem is to find the best possible alignment between a succeeding factor of the reference sequence and the remaining low-quality part of the read; allowing a number of mismatches and the insertion of gaps in the alignment. Results: We present GapsMis, a tool for pairwise global and semi-global sequence alignment with a variable, but bounded, number of gaps. It is based on a new algorithm, which computes a different version of the traditional dynamic programming matrix. Millions of pairwise sequence alignments, performed under realistic conditions based on the properties of real full-length genomes, show that GapsMis can increase the accuracy of extending short-read alignments end-to-end compared to more traditional approaches. Availability: http://www.exelixis-lab.org/gapmis