Fast and practical algorithms for planted (l, d) motif search.
IEEE/ACM Trans Comput Biol Bioinform
; 4(4): 544-52, 2007.
Article
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| MEDLINE
| ID: mdl-17975266
We consider the planted (l, d) motif search problem, which consists of finding a substring of length l that occurs in a set of input sequences {s1, . . . , sn} with up to d errors, a problem that arises from the need to find transcription factor-binding sites in genomic information. We propose a sequence of practical algorithms, which start based on the ideas considered in PMS1. These algorithms are exact, have little space requirements, and are able to tackle challenging instances with bigger d, taking less time in the instances reported solved by exact algorithms. In particular, one of the proposed algorithms, PMSprune, is able to solve the challenging instances, such as (17, 6) and (19, 7), which were not previously reported as solved in the literature.
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Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Biología Computacional
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
ACM Trans Comput Biol Bioinform
Asunto de la revista:
BIOLOGIA
/
INFORMATICA MEDICA
Año:
2007
Tipo del documento:
Article
País de afiliación:
Estados Unidos
Pais de publicación:
Estados Unidos