Advances in Bioinformatics and Computational Biology: 4th by Katia S. Guimarães, Anna Panchenko, Teresa M. Przytycka

By Katia S. Guimarães, Anna Panchenko, Teresa M. Przytycka

This booklet constitutes the refereed court cases of the 4th Brazilian Symposium on Bioinformatics, BSB 2009, held in Porto Alegre, Brazil, in July 2009.

The 12 revised complete papers and six prolonged abstracts have been rigorously reviewed and chosen from fifty five submissions. The papers are prepared in topical sections on algorithmic methods for molecular biology difficulties; micro-array research; computer studying equipment for class; and in silico simulation.

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Additional info for Advances in Bioinformatics and Computational Biology: 4th Brazilian Symposium on Bioinformatics, BSB 2009, Porto Alegre, Brazil, July 29-31, 2009, Proceedings

Example text

Moreover, peaks corresponding to dependent ions are called dependent peaks. Fig. 1. This figure shows the fragmentation points inside a peptide containing four amino acids (AAi with i ∈ [1; 4]). Ri (i ∈ [1; 4]) are chemical compounds that determine the corresponding amino acid. In this example, there are three sets of dependent ions. We can notice that a symmetry exists between N-terminal and C-terminal peaks for a given fragmentation. In Figure 2 (a), the N-terminal peak located at position m(GL) and the C-terminal peak located at position m(M P RG) are linked by the relation m(M P RG) = m(GLM P RG) − m(GL) − 20 (−20 is due to the fact that the peptide is not symmetric at its extremities, see Figure 1, and to the ionization).

In this context, a new multi-objective evolutionary approach for microarray biclustering is presented, which mixes an aggregative evolutionary algorithm with features that enhance its natural capabilities. To the best of our knowledge, this methodology introduces two novel features that were never addressed, or partially dealt-with, by other evolutionary techniques designed for this problem instance. The first contribution consists in the design of a recovery process that extracts the best solutions through the generations.

According to their definition, a bicluster is a group of rows whose values induce a linear order across a subset of the columns. The work focuses on the relative order of the columns in the bicluster rather than on the uniformity of the actual values in the data matrix. More specifically, they want to identify large OPSMs. A submatrix is order-preserving if there is a permutation of its columns under which the sequence of values in every row is strictly increasing. In this way, Ben-Dor et al. aim at finding a complete model with highest statistically significant support.

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