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

Author(s): Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis, German Tischler.

Journal Name: Recent Patents on DNA & Gene Sequences (Discontinued)

Volume 7 , Issue 2 , 2013


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.

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Article Details

Year: 2013
Page: [84 - 95]
Pages: 12
DOI: 10.2174/1872215611307020002
Price: $58

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