Advances in Bioinformatics and Computational Biology: 6th by David Langenberger, Sebastian Bartschat, Jana Hertel, Steve

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

This e-book 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 provided have been conscientiously peer-reviewed and chosen for inclusion during this booklet. The BSB subject matters of curiosity disguise many parts of bioinformatics that diversity from theoretical features 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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In other words, if u is an internal node of Ti−2 , then its suffix link is present in Ti−1 . Besides that, all the leaves of Ti−2 also have their suffix links present. This proves the next corollary. Corollary 1. Let u be a vertex of Ti−1 already present in Ti−2 . Suppose that there is some j ∈ [1, m] such that fj ∈ Pref(u). e. the suffix link of u is present in Ti−1 . 1 The proof is omited due to space restrictions, but it can be found in [9]. T. P. do Lago The Algorithm In this section we present an algorithm that builds the sparse suffix tree for any set of suffixes, such that the corresponding set of factors satisfies Hypothesis 1.

Finally, in Definition 1 we present the Ukkonen’s tree of W , a very special case of A+ -tree. Definition 1 (Ukkonen’s tree). Given a set of words W , the Ukkonen’s tree of W is the A+ -tree T = (V, E, λ) where: V = W ∪ Bifurc(W ) ∪ {1}, E = {(u, v) ∈ V × V | u = max|x| {x ∈ V | x is a proper prefix of v}}, λ:E −→ A+ (u, v) −→ u−1 v. The proof that the Ukkonen’s tree is in fact an A+ -tree, along with more detailed exposition of the properties Ukkonen’s tree, can be found in [9,7]. The suffix tree of W is the Ukkonen’s tree of Suf(W ).

In this study, for the RandomForest and ADTree algorithms, we presented the results obtained from the combination of parameter values that produced the best predictive accuracy performance. The experimental results for the datasets D1 , D2 and D3 are shown in Figure 1. 87%. However, for all classifiers, the datasets D2 and D3 reached better predictive accuracies when compared with those obtained for the dataset D1 , indicating that the addition of resistance levels to antiretroviral drugs, HIV subtype and epitope attributes contributes to enhance the accuracy of the classifiers.

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