By Luís Felipe I. Cunha, Luis Antonio B. Kowada (auth.), Marcilio C. de Souto, Maricel G. Kann (eds.)
This publication constitutes the refereed complaints of the seventh Brazilian Symposium on Bioinformatics, BSB 2012, held in Campo Grande, Brazil, in August 2012. The sixteen common papers provided have been rigorously reviewed and chosen for inclusion during this publication. It additionally features a joint paper from of the visitor audio system. The Brazilian Symposium on Bioinformatics covers all facets of bioinformatics and computational biology, together with series research; motifs, and trend matching; organic databases, information administration, info integration, and information mining; biomedical textual content mining; structural, comparative, and practical genomics; own genomics; protein constitution, modeling, and simulation; gene identity, rules and expression research; gene and protein interplay and networks; molecular docking; molecular evolution and phylogenetics; computational platforms biology; computational proteomics; statistical research of molecular sequences; algorithms for difficulties in computational biology; purposes in molecular biology, biochemistry, genetics, drugs, microbiology and linked subjects.
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Extra info for Advances in Bioinformatics and Computational Biology: 7th Brazilian Symposium on Bioinformatics, BSB 2012, Campo Grande, Brazil, August 15-17, 2012. Proceedings
9]). In these circumstances it may be preferable to ﬁnd more tractable measures for comparing parsings. The three criteria we propose are heuristic, and are intended as easily computed surrogates for the score of the maximum parsimony tree. They are each based on the observation that the histories of two nucleotide substitutions that occur at nearby sites less than bases apart at some stage in the evolution of the tandem repeat can be diﬀerent depending on whether they occur in the same or adjacent copies of the motif.
The number of motifs copied is referred to as the size of the duplication. We assume that the boundaries of a duplication event fall on the boundaries of a repeat. A. Matroud et al. c c c e CATGGT f 3γ 5β 5β f 3α ←root e 3α 3β a o 3α a 3γ o 1α 1α a d o 6β 6β o 5β 1α d b b c f 3γ o 6β a b (a) (b) b a b c c d e f (c) Fig. 1. In (a) we see a graph connecting the 6 variants in (2), with each edge u, v labelled by the substitution iθ that transforms u to v. (b) Arbitrarily breaking the cycle, and adding leaves for the multiple segments, we obtain a maximum parsimony tree of the 9 segments.
14]; Hauth and Joseph ; Stoye and Gusﬁeld ; Benson ; Sagot and Myers ). To the best of our knowledge the only reference on this problem to date is by Benson and Dong , who propose a method to solve the parsing problem based on a tandem repeat duplication model which allows dynamic boundaries (that is, duplications may occur on different boundaries throughout the duplication history). The purpose of this paper is to present three new criteria to select the parsing, under the assumption that the pattern boundaries are ﬁxed throughout the duplication process (Fitch ).