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Bounded-length Smith-Waterman alignment
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Tiskin, Alexander (2019) Bounded-length Smith-Waterman alignment. In: 19th International Workshop on Algorithms in Bioinformatics (WABI 2019), Niagara Falls, NY, USA, 8-10 Sep 2019, 143 16:1-16:12. ISBN 9783959771238. ISSN 1868-8969. doi:10.4230/LIPIcs.WABI.2019.16
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Official URL: http://doi.org/10.4230/LIPIcs.WABI.2019.16
Abstract
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 Egecioglu under the name "local alignment with length threshold". They proposed a dynamic programming algorithm solving the problem in time O(mn^2), 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.
| Item Type: | Conference Item (Paper) | ||||
|---|---|---|---|---|---|
| Subjects: | Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software Q Science > QH Natural history |
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| Divisions: | Faculty of Science > Computer Science | ||||
| Library of Congress Subject Headings (LCSH): | Sequence alignment (Bioinformatics), Computer algorithms, Molecular biology -- Data processing | ||||
| Series Name: | Leibniz International Proceedings in Informatics (LIPIcs) | ||||
| Publisher: | Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik | ||||
| Place of Publication: | Dagstuhl, Germany | ||||
| ISBN: | 9783959771238 | ||||
| ISSN: | 1868-8969 | ||||
| Official Date: | 17 June 2019 | ||||
| Dates: |
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| Volume: | 143 | ||||
| Page Range: | 16:1-16:12 | ||||
| Article Number: | 16 | ||||
| DOI: | 10.4230/LIPIcs.WABI.2019.16 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Open Access | ||||
| Copyright Holders: | Alexander Tiskin | ||||
| Conference Paper Type: | Paper | ||||
| Title of Event: | 19th International Workshop on Algorithms in Bioinformatics (WABI 2019) | ||||
| Type of Event: | Conference | ||||
| Location of Event: | Niagara Falls, NY, USA | ||||
| Date(s) of Event: | 8-10 Sep 2019 | ||||
| Related URLs: | |||||
| Open Access Version: |
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