A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolataстатья

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Дата последнего поиска статьи во внешних источниках: 15 декабря 2016 г.

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[1] A method for identification of highly conserved elements and evolutionary analysis of superphylum alveolata / L. I. Rubanov, A. V. Seliverstov, O. A. Zverkov, V. A. Lyubetsky // BMC Bioinformatics. — 2016. — Vol. 17, no. 285. — P. 16. A novel algorithm is developed to identify highly conserved DNA elements. It is based on the identification of dense subgraphs in a specially built multipartite graph (whose parts correspond to genomes). Specifically, the algorithm does not rely on genome alignments, nor pre-identified perfectly conserved elements; instead, it performs a fast search for pairs of words (in different genomes) of maximum length with the difference below the specified edit distance. Such pair defines an edge whose weight equals the maximum (or total) length of words assigned to its ends. The graph composed of these edges is then compacted by merging some of its edges and vertices. The dense subgraphs are identified by a cellular automaton-like algorithm; each subgraph defines a cluster composed of similar inextensible words from different genomes. Almost all clusters are considered as predicted highly conserved elements. The algorithm is applied to the nuclear genomes of the superphylum Alveolata, and the corresponding phylogenetic tree is built and discussed. [ DOI ]

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