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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