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Recent Patents on DNA & Gene Sequences
ISSN (Print): 1872-2156
ISSN (Online): 2212-3431
VOLUME: 7
ISSUE: 2
DOI: 10.2174/1872215611307020002      Price:  $100









GapMis: a Tool for Pairwise Sequence Alignment with a Single Gap

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Author(s): Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis and German Tischler
Pages 84-95 (12)
Abstract:
Motivation: Pairwise sequence alignment has received a new motivation due to the advent of recent patents in next-generation sequencing technologies, 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 a high-quality fragment of a short read by a short-read alignment programme, an important problem is to find the alignment between a relatively short succeeding factor of the reference sequence and the remaining low-quality part of the read allowing a number of mismatches and the insertion of a single gap in the alignment. Results: We present GapMis, a tool for pairwise sequence alignment with a single gap. It is based on a simple algorithm, which computes a different version of the traditional dynamic programming matrix. The presented experimental results demonstrate that GapMis is more suitable and efficient than most popular tools for this task.
Keywords:
Pairwise sequence alignment, gap, read mapping.
Affiliation:
Heidelberg Institute for Theoretical Studies, Germany.