By Marie-France Sagot, Maria Emilia M.T. Walter

This publication constitutes the refereed complaints of the second one Brazilian Symposium on Bioinformatics, BSB 2007, held in Angra dos Reis, Brazil, in August 2007; co-located with IWGD 2007, the overseas Workshop on Genomic Databases.

The thirteen revised complete papers and six revised prolonged abstracts have been rigorously reviewed and chosen from 60 submissions. The papers tackle a large variety of present subject matters in computationl biology and bioinformatics that includes unique study in computing device technology, arithmetic and statistics in addition to in molecular biology, biochemistry, genetics, drugs, microbiology and different existence sciences.

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Additional info for Advances in Bioinformatics and Computational Biology: Second Brazilian Symposium on Bioinformatics, BSB 2007, Angra dos Reis, Brazil, August 29-31,

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Therefore, we decided to use the information gain. 4 Experiments In order to evaluate our approach, we choose datasets that contain more than E one possible structure. , π En } is the set of known structures E for a given dataset, where n is the number of known structures and π Ej is the jth known structure. Three artificial and two real datasets were employed. Table 1 summarizes the main characteristics of the datasets. In this table, n is the number of objects, d is the dimension of the dataset (number of attributes), nE is the number of known structures and K Ej is the number of clusters of the jth structure.

18] and to the ones produced by Waterman et al. [22]. In [4] an algorithm based on random projections of the motif is proposed. Constructed under the planted motif model, this algorithm obtains a good performance compared with the commonly used methods like Gibbs [11] and MEME [1]. In [23] the Motif Finding Problem is defined as to find a local alignment of multiple sequences without gaps using the sum-of-pairs scoring scheme and the filogenetic distance. Combinatorial techniques like branch pruning and linear programming are used to solve the problem.

Brizuela Computer Sciences Department CICESE Research Center Km 107 Carr. mx +52–646–175–0500 Abstract. The DNA motif finding problem is of great relevance in molecular biology. Weak signals that mark transcription factor binding sites involved in gene regulation are considered to be challenging to find. These signals (motifs) consist of a short string of unknown length that can be located anywhere in the gene promoter region. Therefore, the problem consists on discovering short, conserved sites in genomic DNA without knowing, a priori, the length nor the chemical composition of the site, turning the original problem into a combinatorial one, where computational tools can be applied to find the solution.

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