TY - GEN
T1 - GapMis-OMP
T2 - 8th International Workshop on Artificial Intelligence Applications and Innovations, AIAI 2012: AIAB, AIeIA, CISE, COPA, IIVC, ISQL, MHDW, and WADTMB
AU - Flouri, Tomáš
AU - Iliopoulos, Costas S.
AU - Park, Kunsoo
AU - Pissis, Solon P.
PY - 2012/1/1
Y1 - 2012/1/1
N2 - Pairwise sequence alignment has received a new motivation due to the advent of 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 fragment of the read allowing a number of mismatches and the insertion of a single gap in the alignment. In this article, we present GapMis-OMP, a tool for pairwise short-read alignment that works on multi-core architectures. It is designed to compute the alignments between all the sequences in a first set of sequences and all those from a second one in parallel. The presented experimental results demonstrate that GapMis-OMP is more efficient than most popular tools.
AB - Pairwise sequence alignment has received a new motivation due to the advent of 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 fragment of the read allowing a number of mismatches and the insertion of a single gap in the alignment. In this article, we present GapMis-OMP, a tool for pairwise short-read alignment that works on multi-core architectures. It is designed to compute the alignments between all the sequences in a first set of sequences and all those from a second one in parallel. The presented experimental results demonstrate that GapMis-OMP is more efficient than most popular tools.
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U2 - 10.1007/978-3-642-33412-2_61
DO - 10.1007/978-3-642-33412-2_61
M3 - Conference contribution
AN - SCOPUS:84870877393
SN - 9783642334115
T3 - IFIP Advances in Information and Communication Technology
SP - 593
EP - 601
BT - Artificial Intelligence Applications and Innovations - AIAI 2012 International Workshops
PB - Springer New York LLC
Y2 - 27 September 2012 through 30 September 2012
ER -