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Literature DB >> 23959399

PMS6: A Fast Algorithm for Motif Discovery.

Shibdas Bandyopadhyay¹, Sartaj Sahni, Sanguthevar Rajasekaran.

Abstract

We propose a new algorithm, PMS6, for the (l, d)-motif discovery problem in which we are to find all strings of length l that appear in every string of a given set of strings with at most d mismatches. The run time ratio PMS5/PMS6, where PMS5 is the fastest previously known algorithm for motif discovery in large instances, ranges from a high of 2.20 for the (21,8) challenge instances to a low of 1.69 for the (17,6) challenge instances. Both PMS5 and PMS6 require some amount of preprocessing. The preprocessing time for PMS6 is 34 times faster than that for PMS5 for (23,9) instances. When preprocessing time is factored in, the run time ratio PMS5/PMS6 is as high as 2.75 for (13,4) instances and as low as 1.95 for (17,6) instances.

Entities: Chemical Gene Species

Keywords: Planted motif search; string algorithms

Year: 2012 PMID： 23959399 PMCID： PMC3744182 DOI： 10.1109/ICCABS.2012.6182627

Source DB: PubMed Journal: IEEE Int Conf Comput Adv Bio Med Sci ISSN： 2164-229X

12 in total

1. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.

Authors: G Z Hertz; G D Stormo
Journal: Bioinformatics Date: 1999 Jul-Aug Impact factor: 6.937

2. Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification.

Authors: L Marsan; M F Sagot
Journal: J Comput Biol Date: 2000 Impact factor: 1.479

PMS6: A Fast Algorithm for Motif Discovery.

1. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.

2. Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification.

3. Finding motifs in the twilight zone.

4. Finding composite regulatory patterns in DNA sequences.

5. Exact algorithms for planted motif problems.

6. Fast and practical algorithms for planted (l, d) motif search.

7. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment.

8. PMS5: an efficient exact algorithm for the (ℓ, d)-motif finding problem.

9. Efficient motif finding algorithms for large-alphabet inputs.

10. A speedup technique for (l, d)-motif finding algorithms.

1. PMS6MC: A Multicore Algorithm for Motif Discovery.

2. Efficient algorithms for biological stems search.