Download Advances in Bioinformatics and Computational Biology: 8th by Fabian Amman, Stephan H. Bernhart (auth.), João C. Setubal, PDF

By Fabian Amman, Stephan H. Bernhart (auth.), João C. Setubal, Nalvo F. Almeida (eds.)

This booklet constitutes the refereed lawsuits of the eighth Brazilian Symposium on Bioinformatics, BSB 2013, held in Recife, Brazil, in November 2013. The 18 normal papers awarded have been rigorously reviewed and chosen for inclusion during this ebook. The papers hide all features of bioinformatics and computational biology.

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Additional resources for Advances in Bioinformatics and Computational Biology: 8th Brazilian Symposium on Bioinformatics, BSB 2013, Recife, Brazil, November 3-7, 2013, Proceedings

Example text

Given two linear genomes A and B without duplicated markers, we have d rDCJ-id (A, B) = dDCJ-id (A, B). Observe that Theorem 1 holds even if we assign the cost of 1 to each DCJ and a positive cost w ≤ 1 to each indel operation. Complexity. For any positive indel cost w ≤ 1, the DCJ-indel distance can be computed in linear time [15, 20], and thus the same is true for the restricted DCJ-indel distance. Establishing the triangular inequality. Obviously the correction proposed in [15, 21] to establish the triangular inequality for the DCJ-indel distance also holds for the restricted DCJ-indel distance.

As said before, unfortunately the HIPP problem is NP-hard [8]. Some approaches based on Integer Programming have been proposed for it [9] [10] [11] [12]. Another method for the HIPP problem is the Parsimonious Tree-Grow (PTG) method [13], which explains a set of m genotypes of length n in time O(m2 n). S. S. Guimar˜ aes by haplotypes formatted by a trace from the root to that specific node. Many operations in PTG are random, so it is necessary to run the method many times, selecting the best solution using some metric, in order to have reliable results.

C Springer International Publishing Switzerland 2013 Restricted DCJ-Indel Model Revisited 37 Computing the DCJ distance and finding one optimal DCJ sorting scenario can be done in linear time [8]. However, while sorting a genome into another by DCJ, circular chromosomes can appear in the intermediate steps [7, 8]. In the general model many circular chromosomes can coexist in some intermediate step, even if the compared genomes are composed of linear chromosomes only, such as eukaryotic nuclear genomes.

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