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By David Langenberger, Sebastian Bartschat, Jana Hertel, Steve Hoffmann, Hakim Tafer (auth.), Osmar Norberto de Souza, Guilherme P. Telles, Mathew Palakal (eds.)

This booklet constitutes the lawsuits of the sixth Brazilian Symposium on Bioinformatics, BSB 2011, held in Brasília, Brazil, in August 2011.
The eight complete papers and four prolonged abstracts offered have been conscientiously peer-reviewed and chosen for inclusion during this e-book. The BSB issues of curiosity hide many parts of bioinformatics that variety from theoretical points of difficulties in bioinformatics to functions in molecular biology, biochemistry, genetics, and linked subjects.

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Extra info for Advances in Bioinformatics and Computational Biology: 6th Brazilian Symposium on Bioinformatics, BSB 2011, Brasilia, Brazil, August 10-12, 2011. Proceedings

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The first one, presented by Andersson et al. [1] is not a practical alternative, it is very complex and has a very high time constant. On the other hand, the algorithm of Inenaga et al. [5] based on Ukkonen’s algorithm, can be used in practice. 2 Definitions Let w be a word (or string) over the finite alphabet A. The length of w is denoted by |w|. The same notation also is used for set cardinality, for instance the size of the alphabet is |A|. The set of all possible words over A, including the empty word 1, is given by A∗ and the set A∗ \ {1} is denoted by A+ .

These datasets, named D1 , D2 and D3 , are composed by the following predictive attributes: 1) D1 : HIV mutations, viral load and CD4+ cell counts; 2) HIV mutations, viral load, CD4+ cell counts and antiretroviral drug resistance levels; 3) HIV mutations, viral load, CD4+ cell counts, resistance levels to antiretroviral drugs, length of RT and PR sequence, similarity of RT and PR considering their reference sequences, HIV subtype and epitope. Other six datasets were generated from the attribute selection process.

E. hi . The place (ui , xi ) of hi could be in a vertex (xi = 1) or in the middle of an edge (xi = 1) (see Fig. 1). If it is the latter, we A New Algorithm for Sparse Suffix Trees 37 ui ui = hi xi hi ti ti w(i, m) (a) vi w(i, m) (b) Fig. 1. These figures illustrate the tree Ti−1 after the update to Ti , for the two possible cases: (a) The place (ui , xi ) of hi is in a vertex; (b) The place (ui , xi ) is in an edge break the edge in xi and add a vertex with label hi in that place. Finally, we add an edge with label ti from the vertex ui and the new leave w(i, m).

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