论文信息 - Space and Time Efficient Algorithms for Planted Motif Search

Space and Time Efficient Algorithms for Planted Motif Search

We consider the (l,d) Planted Motif Search Problem, a problem that arises from the need to find transcription factor-binding sites in genomic information. We propose the algorithms PMSi and PMSP which are based on ideas considered in PMS1 [10]. These algorithms are exact, make use of less space than the known exact algorithms such as PMS and are able to tackle instances with large values of d. In particular algorithm PMSP is able to solve the challenge instance (17,6), which has not reported solved before in the literature.

Sanguthevar Rajasekaran | Jaime I. Dávila | Sudha Balla | S. Rajasekaran | S. Balla

[1] Eleazar Eskin,et al. Finding composite regulatory patterns in DNA sequences , 2002, ISMB.

[2] Andrew D. Smith,et al. Toward Optimal Motif Enumeration , 2003, WADS.

[3] Sriram Ramabhadran,et al. Finding subtle motifs by branching from sample strings , 2003, ECCB.

[4] Jeremy Buhler,et al. Finding motifs using random projections , 2001, RECOMB.

[5] Todd Wareham,et al. On the complexity of finding common approximate substrings , 2003, Theor. Comput. Sci..

[6] Jianer Chen,et al. Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding , 2004, WABI.

[7] Bin Ma,et al. On the closest string and substring problems , 2002, JACM.

[8] Sanguthevar Rajasekaran,et al. Exact Algorithms for Planted Motif Problems , 2005, J. Comput. Biol..

[9] Pavel A. Pevzner,et al. Combinatorial Approaches to Finding Subtle Signals in DNA Sequences , 2000, ISMB.

[10] Francis Y. L. Chin,et al. Voting algorithms for discovering long motifs , 2005, APBC.