SA-REPC - Sequence alignment with regular expression path constraint

Nimrod Milo, Tamar Pinhas, Michal Ziv-Ukelson

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

1 Scopus citations


In this paper, we define a novel variation on the constrained sequence alignment problem, the Sequence Alignment with Regular Expression Path Constraint problem, in which the constraint is given in the form of a regular expression. Our definition extends and generalizes the existing definitions of alignment-path constrained sequence alignments to the expressive power of regular expressions. We give a solution for the new variation of the problem and demonstrate its application to integrate microRNA-target interaction patterns into the target prediction computation. Our approach can serve as an efficient filter for more computationally demanding target prediction filtration algorithms. We compare our implementation for the SA-REPC problem, cAlign, to other microRNA target prediction algorithms.

Original languageEnglish
Title of host publicationLanguage and Automata Theory and Applications - 4th International Conference, LATA 2010, Proceedings
Number of pages12
StatePublished - 25 Jun 2010
Event4th International Conference on Language and Automata Theory and Applications, LATA 2010 - Trier, Germany
Duration: 24 May 201028 May 2010

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6031 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference4th International Conference on Language and Automata Theory and Applications, LATA 2010

ASJC Scopus subject areas

  • Theoretical Computer Science
  • General Computer Science


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