GapMis: a Tool for Pairwise Sequence Alignment with a Single Gap
Tomas Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis and German Tischler
Pages 84-95 (12)
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.
Pairwise sequence alignment, gap, read mapping.
Heidelberg Institute for Theoretical Studies, Germany.