Efficient sequential and parallel 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 [6]. 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. ...

CORRIGENDUM: qPMS9: An Efficient Algorithm for Quorum Planted Motif Search

qPMS9: An Efficient Algorithm for Quorum Planted Motif Search

Discovering patterns in biological sequences is a crucial problem. For example, the identification of patterns in DNA sequences has resulted in the determination of open reading frames, identification of gene promoter elements, intron/exon splicing sites, and SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have led ...

Exact algorithms for planted motif challenge problems

The problem of identifying meaningful patterns (i.e., motifs) from biological data has been studied extensively due to its paramount importance. Three versions of this problem have been identified in the literature. One of these three problems is the planted (l, d)-motif problem. Several instances of this problem have been posed as a challenge. Numerous algorithms have been proposed in the lite...

Algorithms for Motif Search

University of Connecticut 1.1 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1 1.2 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1 1.3 Algorithms for Planted Motif Search . . . . . . . . . . . . . . . 1-2 A Probabilistic Analysis • The WINNOWER and SP-STAR Algorithms • Pattern Br...