Download Algorithms in Bioinformatics: 11th International Workshop, by Broňa Brejová, Michal Burger, Tomáš Vinař (auth.), Teresa M. PDF

By Broňa Brejová, Michal Burger, Tomáš Vinař (auth.), Teresa M. Przytycka, Marie-France Sagot (eds.)

This booklet constitutes the refereed court cases of the eleventh overseas Workshop on Algorithms in Bioinformatics, WABI 2011, held in Saarbrücken, Germany, in September 2011.
The 30 papers awarded have been rigorously reviewed and chosen from seventy seven submissions. They hide facets of algorithms in bioinformatics, computational biology and structures biology.

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Additional info for Algorithms in Bioinformatics: 11th International Workshop, WABI 2011, Saarbrücken, Germany, September 5-7, 2011. Proceedings

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In order to solve a problem instance, we iteratively consider combinations of (F, G) starting from F = LB crs and G = 1+ log2 F . In addition we enforce that Marker-Assisted Gene Pyramiding 31 the objective value of any feasible solution must be better than the currently best one. We do this by computing an upper bound UB pop on the total population size, based on the best objective value found so far and the current values of (F, G) (see Algorithm 1, line 4). If at some point, say (F , G ), LB pop ≥ UB pop then we know that none of the combinations of F ≥ F , G ≥ G will lead to a better solution.

Contrary to our expectations, this approach did not provide satisfactory results. This may be because the diameter of the inferred quartets varies widely between different levels of the search tree. Quartets inferred near the root of the search tree tend to have large distances between taxa, whereas quartets inferred in the deeper parts of the search tree are shorter since they only span a small fraction of the overall tree. Using least squares fit Towards a Practical O(n log n) Phylogeny Algorithm 21 of the distances to the quartet topology also did not seem to improve the accuracy of node queries, and using weighted least squares also did not improve the accuracy of quartet inferences.

For example, maximal-length contigs from the graph in Figure 1 are {ab → bc → cd, cd → de → ef → f c → cd, cd → dg → gh}. In contrast, a non-trivial non-branching path is {ab ef gh}, where the path-string (ab♦2 ef ♦2 gh) is a scaffold which covers the whole string. Under ideal sequencing conditions, non-branching paths immediately correspond to valid scaffolds. One can also consider in- (resp. out-) branching paths, for which only out- (resp. in-) degree of nodes in the path with respect to the corresponding edge type is 1.

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