منابع مشابه
Efficient exact motif discovery
MOTIVATION The motif discovery problem consists of finding over-represented patterns in a collection of biosequences. It is one of the classical sequence analysis problems, but still has not been satisfactorily solved in an exact and efficient manner. This is partly due to the large number of possibilities of defining the motif search space and the notion of over-representation. Even for well-d...
متن کاملDevelopment of an Efficient Hybrid Method for Motif Discovery in DNA Sequences
This work presents a hybrid method for motif discovery in DNA sequences. The proposed method called SPSO-Lk, borrows the concept of Chebyshev polynomials and uses the stochastic local search to improve the performance of the basic PSO algorithm as a motif finder. The Chebyshev polynomial concept encourages us to use a linear combination of previously discovered velocities beyond that proposed b...
متن کاملAn 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...
متن کاملAlgorithms and statistical methods for exact motif discovery
The motif discovery problem consists of uncovering exceptional patterns (called motifs) in sets of sequences. It arises in molecular biology when searching for yet unknown functional sites in DNA sequences. In this thesis, we develop a motif discovery algorithm that (1) is exact, that means it returns a motif with optimal score, (2) can use the statistical significance with respect to complex b...
متن کاملdevelopment of an efficient hybrid method for motif discovery in dna sequences
this work presents a hybrid method for motif discovery in dna sequences. the proposed method called spso-lk, borrows the concept of chebyshev polynomials and uses the stochastic local search to improve the performance of the basic pso algorithm as a motif finder. the chebyshev polynomial concept encourages us to use a linear combination of previously discovered velocities beyond that proposed b...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2009
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btp188