title: GapMis: a tool for pairwise sequence alignment with a single gap.
abstract: BACKGROUND
  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.
authors.affiliation: Czech Technical University in Prague, Dept. of Theoretical Computer Science, Czech Republic.
authors.forename: Tomás
authors.initials: T
authors.lastname: Flouri
authors.forename: Kimon
authors.initials: K
authors.lastname: Frousios
authors.forename: Costas S
authors.initials: CS
authors.lastname: Iliopoulos
authors.forename: Kunsoo
authors.initials: K
authors.lastname: Park
authors.forename: Solon P
authors.initials: SP
authors.lastname: Pissis
authors.forename: German
authors.initials: G
authors.lastname: Tischler
mesh_terms: D000465:Algorithms; D059014:High-Throughput Nucleotide Sequencing; D010330:Patents as Topic; D016415:Sequence Alignment; D012984:Software