PMS6MC: A Multicore Algorithm for Motif Discovery
نویسندگان
چکیده
منابع مشابه
An Efficient Algorithm for String Motif Discovery
Finding common patterns, motifs, in a set of DNA sequences is an important problem in bioinformatics. One common representation of motifs is a string with symbols A, C, G, T and N where N stands for the wildcard symbol. In this paper, we introduce a more general motif discovery problem without any weaknesses of the Planted (l,d)-Motif Problem and also a set of control sequences as an additional...
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MOTIVATION Motif discovery in sequential data is a problem of great interest and with many applications. However, previous methods have been unable to combine exhaustive search with complex motif representations and are each typically only applicable to a certain class of problems. RESULTS Here we present a generic motif discovery algorithm (Gemoda) for sequential data. Gemoda can be applied ...
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We study a natural probabilistic model for motif discovery that has been used to experimentally test the quality of motif discovery programs. In this model, there are k background sequences, and each character in a background sequence is a random character from an alphabet Σ. A motif G = g1g2 · · · gm is a string of m characters. Each background sequence is implanted into a probabilistically ge...
متن کاملTree-structured algorithm for long weak motif discovery
MOTIVATION Motifs in DNA sequences often appear in degenerate form, so there has been an increased interest in computational algorithms for weak motif discovery. Probabilistic algorithms are unable to detect weak motifs while exact methods have been able to detect only short weak motifs. This article proposes an exact tree-based motif detection (TreeMotif) algorithm capable of discovering longe...
متن کاملHybrid Gibbs-sampling algorithm for challenging motif discovery: GibbsDST.
The difficulties of computational discovery of transcription factor binding sites (TFBS) are well represented by (l, d) planted motif challenge problems. Large d problems are difficult, particularly for profile-based motif discovery algorithms. Their local search in the profile space is apparently incompatible with subtle motifs and large mutational distances between the motif occurrences. Here...
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ژورنال
عنوان ژورنال: Algorithms
سال: 2013
ISSN: 1999-4893
DOI: 10.3390/a6040805