TY - GEN
T1 - Bit-parallel algorithm for the block variant of the merged longest common subsequence problem
AU - Danek, Agnieszka
AU - Deorowicz, Sebastian
N1 - Publisher Copyright:
© Springer International Publishing Switzerland 2014.
PY - 2014
Y1 - 2014
N2 - The problem of comparison of genomic sequences is of great importance. There are various measures of similarity of sequences. One of the most popular is the length of the longest common subsequence (LCS). We propose the first bitparallel algorithm for the variant of the LCS problem, block merged LCS, which was recently formulated in the studies on the whole genome duplication hypothesis. Practical experiments show that our proposal is from 10 to over 100 times faster than existing algorithms.
AB - The problem of comparison of genomic sequences is of great importance. There are various measures of similarity of sequences. One of the most popular is the length of the longest common subsequence (LCS). We propose the first bitparallel algorithm for the variant of the LCS problem, block merged LCS, which was recently formulated in the studies on the whole genome duplication hypothesis. Practical experiments show that our proposal is from 10 to over 100 times faster than existing algorithms.
KW - Genome
KW - Longest common subsequence
KW - Sequence comparison
UR - https://www.scopus.com/pages/publications/84927649450
U2 - 10.1007/978-3-319-02309-0_18
DO - 10.1007/978-3-319-02309-0_18
M3 - Conference contribution
AN - SCOPUS:84927649450
T3 - Advances in Intelligent Systems and Computing
SP - 173
EP - 181
BT - Man-Machine Interactions 3
A2 - Gruca, Aleksandra
A2 - Czachórski, Tadeusz
A2 - Kozielski, Stanisław
A2 - Czachórski, Tadeusz
PB - Springer Verlag
T2 - 3rd International Conference on Man-Machine Interactions, ICMMI 2013
Y2 - 22 October 2013 through 25 October 2013
ER -