Regular language constrained sequence alignment revisited

Gregory Kucherov, Tamar Pinhas, Michal Ziv-Ukelson

Результат исследований: Глава в книге, отчете, сборнике статейМатериалы для конференциирецензирование

Аннотация

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.

Язык оригиналаАнглийский
Название основной публикацииCombinatorial Algorithms - 21st International Workshop, IWOCA 2010, Revised Selected Papers
Страницы404-415
Число страниц12
DOI
СостояниеОпубликовано - 2011
Опубликовано для внешнего пользованияДа
Событие21st International Workshop on Combinatorial Algorithms, IWOCA 2010 - London, Великобритания
Продолжительность: 26 июл. 201028 июл. 2010

Серия публикаций

НазваниеLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Том6460 LNCS
ISSN (печатное издание)0302-9743
ISSN (электронное издание)1611-3349

Конференция

Конференция21st International Workshop on Combinatorial Algorithms, IWOCA 2010
Страна/TерриторияВеликобритания
ГородLondon
Период26/07/1028/07/10

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