DocumentCode
2770875
Title
Extending Pattern Branching to Handle Challenging Instances
Author
Davila, Jorge ; Rajasekaran, Sanguthevar
Author_Institution
Dept. of Comput. Sci. & Eng., Connecticut Univ., Storrs, CT
fYear
2006
fDate
16-18 Oct. 2006
Firstpage
65
Lastpage
69
Abstract
We consider the planted motif search problem, a problem that arises from the need to find transcription factor-binding sites in genomic information. One of the fastest non-exact algorithms that solves this problem is pattern branching [10], however this algorithm fails to solve challenging instances such as (15, 5) in most cases. In this paper we discuss a simple extension to this algorithm and an implementation of it that allows us to tackle challenging instances such as (15, 5) and (17, 6) with accuracy close to 100%
Keywords
biological techniques; biology computing; genetics; search problems; genomic information; instances handling; nonexact algorithms; pattern branching; planted motif search problem; transcription factor-binding sites; Bioinformatics; Computer science; Genomics; Polynomials; Search problems; Voting;
fLanguage
English
Publisher
ieee
Conference_Titel
BioInformatics and BioEngineering, 2006. BIBE 2006. Sixth IEEE Symposium on
Conference_Location
Arlington, VA
Print_ISBN
0-7695-2727-2
Type
conf
DOI
10.1109/BIBE.2006.253317
Filename
4019642
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