TAILIEUCHUNG - Báo cáo sinh học: "Efficient algorithms for the discovery of gapped factors"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Efficient algorithms for the discovery of gapped factors. | Apostolico et al. Algorithms for Molecular Biology 2011 6 5 http content 6 1 5 AMR ALGORITHMS FOR MOLECULAR BIOLOGY RESEARCH Open Access Efficient algorithms for the discovery of gapped factors Alberto Apostolico1 2 Cinzia Pizzi 1 and Esko Ukkonen3 4 Abstract Background The discovery of surprisingly frequent patterns is of paramount interest in bioinformatics and computational biology. Among the patterns considered those consisting of pairs of solid words that co-occur within a prescribed maximum distance -or gapped factors- emerge in a variety of contexts of DNA and protein sequence analysis. A few algorithms and tools have been developed in connection with specific formulations of the problem however none can handle comprehensively each of the multiple ways in which the distance between the two terms in a pair may be defined. Results This paper presents efficient algorithms and tools for the extraction of all pairs of words up to an arbitrarily large length that co-occur surprisingly often in close proximity within a sequence. Whereas the number of such pairs in a sequence of n characters can be 0 n4 it is shown that an exhaustive discovery process can be carried out in O n2 or O n3 depending on the way distance is measured. This is made possible by a prudent combination of properties of pattern maximality and monotonicity of scores which lead to reduce the number of word pairs to be weighed explicitly while still producing also the scores attained by any of the pairs not explicitly considered. We applied our approach to the discovery of spaced dyads in DNA sequences. Conclusions Experiments on biological datasets prove that the method is effective and much faster than exhaustive enumeration of candidate patterns. Software is available freely by academic users via the web interface at http 8080 dyweb. Background The computation of statistical indexes containing subword frequency counts expectations and scores thereof arises .

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