By El-Sayed Bahaa Machaly

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The prediction obtained is finally filtered (with the help of the reliability index) in order to fix some eventually unrealistic local predictions that neither the second level NN nor the consensus were able to detect (particularly, too short alpha-helix segments). The conservation weight provides a score for positions in the MSA with respect to their level of conservation: the more conserved is a position the higher is the conservation weight score. 5) CW i D PN r;sD1 wrs with 1 identrs ; 100 where N is the number of sequences in the multiple alignment, identrs is the percentage of sequence identity (over the entire length) of sequences r; s and simirs is the value of the similarity between sequences r; s at position i according to the Dayhoff similarity matrix [8].

E. Tarjan. A linear time algorithm for testing the truth of certain quantified boolean formulas. Information Processing Letters 8, 121–123 (1979) 2. V. Bafna and N. Edwards. On de novo interpretation of tandem mass spectra for peptide identification. In Annual Conference on Research in Computational Molecular Biology RECOMB03, 9–18 (2003) 22 R. Bruni 3. E. Boros, Y. L. Hammer. Polynomial time inference of all valid implications for Horn and related formulae. Annals of Mathematics and Artificial Intelligence 1, 21–32 (1990) 4.

References 1. B. F. E. Tarjan. A linear time algorithm for testing the truth of certain quantified boolean formulas. Information Processing Letters 8, 121–123 (1979) 2. V. Bafna and N. Edwards. On de novo interpretation of tandem mass spectra for peptide identification. In Annual Conference on Research in Computational Molecular Biology RECOMB03, 9–18 (2003) 22 R. Bruni 3. E. Boros, Y. L. Hammer. Polynomial time inference of all valid implications for Horn and related formulae. Annals of Mathematics and Artificial Intelligence 1, 21–32 (1990) 4.

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