Regular language constrained sequence alignment revisited

Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review


Imposing constraints in the form of a finite automaton or a regular expression is an effective way to incorporate additional a priori knowledge into sequence alignment procedures. With this motivation, Arslan [1] introduced the Regular Language Constrained Sequence Alignment Problem and proposed an O(n 2 t4) time and O(n2 t2) space algorithm for solving it, where n is the length of the input strings and t is the number of states in the non-deterministic automaton, which is given as input. Chung et al. [2] proposed a faster O(n2 t3) time algorithm for the same problem. In this paper, we further speed up the algorithms for Regular Language Constrained Sequence Alignment by reducing their worst case time complexity bound to O(n2 t3/logt). This is done by establishing an optimal bound on the size of Straight-Line Programs solving the maxima computation subproblem of the basic dynamic programming algorithm. We also study another solution based on a Steiner Tree computation. While it does not improve the run time complexity in the worst case, our simulations show that both approaches are efficient in practice, especially when the input automata are dense.

Original languageEnglish
Title of host publicationCombinatorial Algorithms - 21st International Workshop, IWOCA 2010, Revised Selected Papers
Number of pages12
Publication statusPublished - 2011
Externally publishedYes
Event21st International Workshop on Combinatorial Algorithms, IWOCA 2010 - London, United Kingdom
Duration: 26 Jul 201028 Jul 2010

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6460 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference21st International Workshop on Combinatorial Algorithms, IWOCA 2010
Country/TerritoryUnited Kingdom


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