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

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

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

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

Example text

A sequence Γ = (B1 , . . , Bp ) of substrings of S is a chain if B1 ≺ B2 . . ≺ Bp . We denote the concatenation of strings from the chain Γ by Γ ∗ = B1 ∗ B2 ∗ . . ∗ Bp . M. F. S. Adi Finally, given two strings S and T , scorew (S, T ) denotes the score of an optimal alignment between S and T under the scoring function w. With these definitions in mind, the spliced alignment problem can be stated as follows: Spliced Alignment Problem (SAP): given a sequence S = s1 . . sn called subject sequence, a sequence T = t1 .

K−1 πk . . πn ], results in the permutation: πt = [π1 . . πi−1 πj . . πk−1 πi . . πj−1 πk . . πn ]. Notice that a transposition t = (i, j, k) moves the block πj . . πk−1 to the left of the block πi . . πj−1 . We can also generalize this notation to a sequence of transpositions t1 t2 . . tq . Thus, πt1 t2 . . tq denotes the application of t1 onto π, followed by the application of t2 onto πt1 and so on. Given two permutations, the problem of finding a sequence of transpositions that sorts one permutation into the other is called sorting by transpositions.

1] A transposition t applied to a permutation may only increase the number of odd cycles by 2, decrease by 2, or it does not change the number of odd cycles. That is, codd (πt) − codd (π) ∈ {−2, 0, +2}. A transposition that increases the number of odd cycles by 2, decreases by 2, or does not change the number of odd cycles is named, respectively, a 2-move, a (−2)-move or a 0-move. A cycle is said to be oriented if there is a 2-move that affects it. If no 2-move affects a cycle, then it is unoriented.

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