RecMotif: a novel fast algorithm for weak motif discovery
نویسندگان
چکیده
منابع مشابه
Tree-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...
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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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The planted (l, d) motif search is one of the most widely studied problems in bioinformatics, which plays an important role in the identification of transcription factor binding sites in DNA sequences. However, it is still a challenging task to identify highly degenerate motifs, since current algorithms either output the exact results with a high computational cost or accomplish the computation...
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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...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2010
ISSN: 1471-2105
DOI: 10.1186/1471-2105-11-s11-s8