GapMis: A tool for pairwise sequence alignment with a single gap

Tomáš Flouri, Kimon Frousios, Costas S. Iliopoulos, Kunsoo Park, Solon P. Pissis, German Tischler

Research output: Contribution to JournalArticleAcademicpeer-review


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.

Original languageEnglish
Pages (from-to)84-95
Number of pages12
JournalRecent Patents on DNA and Gene Sequences
Issue number2
Publication statusPublished - 28 Aug 2013
Externally publishedYes


  • Gap
  • Pairwise sequence alignment
  • Read mapping


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