Regular Language Constrained Sequence Alignment Revisited
نویسندگان
چکیده
منابع مشابه
Regular Language Constrained Sequence Alignment Revisited
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, the Regular Expression Constrained Sequence Alignment Problem was introduced, which proposed an O(n²t⁴) time and O(n²t²) space algorithm for solving it, where n is the length of the input strings...
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Given strings S1, S2, and a regular expression R, we introduce regular expression constrained sequence alignment as the problem of finding the maximum alignment score between S1 and S2 over all alignments such that in these alignments there exists a segment where some substring s1 of S1 is aligned with some substring s2 of S2, and both s1 and s2 match R, i.e. s1, s2 ∈ L(R) where L(R) is the reg...
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Imposing constraints is an effective means to incorporate biological knowledge into alignment procedures. As in the PROSITE database, functional sites of proteins can be effectively described as regular expressions. In an alignment of protein sequences it is natural to expect that functional motifs should be aligned together. Due to this motivation, Arslan introduced the regular expression cons...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2011
ISSN: 1066-5277,1557-8666
DOI: 10.1089/cmb.2010.0291