Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Research › peer-review
Bounded-length Smith-Waterman alignment. / Tiskin, Alexander.
19th International Workshop on Algorithms in Bioinformatics, WABI 2019. ed. / Katharina T. Huber; Dan Gusfield. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 2019. 16 (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 143).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Research › peer-review
}
TY - GEN
T1 - Bounded-length Smith-Waterman alignment
AU - Tiskin, Alexander
N1 - Publisher Copyright: © Alexander Tiskin; licensed under Creative Commons License CC-BY
PY - 2019/9
Y1 - 2019/9
N2 - Given a fixed alignment scoring scheme, the bounded length (respectively, bounded total length) Smith-Waterman alignment problem on a pair of strings of lengths m, n, asks for the maximum alignment score across all substring pairs, such that the first substring's length (respectively, the sum of the two substrings' lengths) is above the given threshold w. The latter problem was introduced by Arslan and Eğecioğlu under the name “local alignment with length threshold”. They proposed a dynamic programming algorithm solving the problem in time O(mn2), and also an approximation algorithm running in time O(rmn), where r is a parameter controlling the accuracy of approximation. We show that both these problems can be solved exactly in time O(mn), assuming a rational scoring scheme; furthermore, this solution can be used to obtain an exact algorithm for the normalised bounded total length Smith-Waterman alignment problem, running in time O(mn log n). Our algorithms rely on the techniques of fast window-substring alignment and implicit unit-Monge matrix searching, developed previously by the author and others.
AB - Given a fixed alignment scoring scheme, the bounded length (respectively, bounded total length) Smith-Waterman alignment problem on a pair of strings of lengths m, n, asks for the maximum alignment score across all substring pairs, such that the first substring's length (respectively, the sum of the two substrings' lengths) is above the given threshold w. The latter problem was introduced by Arslan and Eğecioğlu under the name “local alignment with length threshold”. They proposed a dynamic programming algorithm solving the problem in time O(mn2), and also an approximation algorithm running in time O(rmn), where r is a parameter controlling the accuracy of approximation. We show that both these problems can be solved exactly in time O(mn), assuming a rational scoring scheme; furthermore, this solution can be used to obtain an exact algorithm for the normalised bounded total length Smith-Waterman alignment problem, running in time O(mn log n). Our algorithms rely on the techniques of fast window-substring alignment and implicit unit-Monge matrix searching, developed previously by the author and others.
KW - Local alignment
KW - Matrix searching
KW - Sequence alignment
KW - Smith-Waterman alignment
UR - http://www.scopus.com/inward/record.url?scp=85072648391&partnerID=8YFLogxK
U2 - 10.4230/LIPIcs.WABI.2019.16
DO - 10.4230/LIPIcs.WABI.2019.16
M3 - Conference contribution
AN - SCOPUS:85072648391
T3 - Leibniz International Proceedings in Informatics, LIPIcs
BT - 19th International Workshop on Algorithms in Bioinformatics, WABI 2019
A2 - Huber, Katharina T.
A2 - Gusfield, Dan
PB - Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
T2 - 19th International Workshop on Algorithms in Bioinformatics, WABI 2019
Y2 - 8 September 2019 through 10 September 2019
ER -
ID: 97181197