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RECOMB
2001
Springer

Finding motifs using random projections

14 years 3 months ago
Finding motifs using random projections
motif discovery problem abstracts the task of discovering short, conserved sites in genomic DNA. Pevzner and Sze recently described a precise combinatorial formulation of motif discovery that motivates the following algorithmic challenge: nd twenty planted occurrences of a motif of length fteen in roughly twelve kilobases of genomic sequence, where each occurrence of the motif differs from its consensus in four randomly chosen positions. Such "subtle" motifs, though statistically highly signi cant, expose a weakness in existing motif- nding algorithms, which typically fail to discover them. Pevzner and Sze introduced new algorithms to solve their (15,4)-motif challenge, but these methods do not scale ef ciently to more dif cult problems in the same family, such as the (14,4)-, (16,5)-, and (18,6)-motif problems. We introduce a novel motif-discovery algorithm, PROJECTION, designed to enhance the performance of existing motif nders using random projections of the input's ...
Jeremy Buhler, Martin Tompa
Added 03 Dec 2009
Updated 03 Dec 2009
Type Conference
Year 2001
Where RECOMB
Authors Jeremy Buhler, Martin Tompa
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