Algorithms in Bioinformatics: 10th International Workshop, by Yelena Frid, Dan Gusfield (auth.), Vincent Moulton, Mona

By Yelena Frid, Dan Gusfield (auth.), Vincent Moulton, Mona Singh (eds.)

This ebook constitutes the refereed lawsuits of the tenth overseas Workshop on Algorithms in Bioinformatics, WABI 2010, held in Liverpool, united kingdom, in September 2010. The 30 revised complete papers awarded have been conscientiously reviewed and chosen from eighty three submissions. The papers are equipped in topical sections on biomolecular constitution: RNA, protein and molecular comparability; comparative genomics; haplotype and genotype research; high-throughput facts research: subsequent iteration sequencing and move cytometry; networks; phylogenetics; and sequences, strings and motifs.

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Additional resources for Algorithms in Bioinformatics: 10th International Workshop, WABI 2010, Liverpool, UK, September 6-8, 2010. Proceedings

Example text

Thus, for the decompositions of all recursion cases there holds such a corresponding inequation. Analogous arguments can be given for all other modified recursion cases. Exemplarily, we elaborate the argument for the complex case 12G21. Let F1 = (i, j − 1; k + 1, l) and F2 = (j , j; k, k ), such RE that (F1 , F2 ) is a split of type 12G21 of (j, j; k, k). We need to show for all T12G21 OD fragments F2 there are non-empty ungapped or 1-gap fragments F1 and F2 , where F1 ∪ F2 = F2 , F1 ∩ F2 = ∅, and W (F1 ∪ F1 ) + W (F2 ) ≥ W (F1 ) + W (F2 ) and the split (F1 ∪ F1 , F2 ) occurs in a recursion case of R&E.

Previous methods for accelerating Tanimoto queries have been based on using bit strings for representing molecules. No work has gone into examining accelerating Tanimoto queries on real valued descriptors, even though these offer a much more fine grained measure of similarity between molecules. This study utilises a recently discovered reduction from Tanimoto queries to distance queries in Euclidean space to accelerate Tanimoto queries using standard metric data structures. The presented experiments show that it is possible to gain a significant speedup and that general metric data structures are better suited than a data structure tailored for Euclidean space on vectors generated from molecular data.

Analogous arguments can be given for all other modified recursion cases. Exemplarily, we elaborate the argument for the complex case 12G21. Let F1 = (i, j − 1; k + 1, l) and F2 = (j , j; k, k ), such RE that (F1 , F2 ) is a split of type 12G21 of (j, j; k, k). We need to show for all T12G21 OD fragments F2 there are non-empty ungapped or 1-gap fragments F1 and F2 , where F1 ∪ F2 = F2 , F1 ∩ F2 = ∅, and W (F1 ∪ F1 ) + W (F2 ) ≥ W (F1 ) + W (F2 ) and the split (F1 ∪ F1 , F2 ) occurs in a recursion case of R&E.

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