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Download e-book for iPad: Algorithms in Bioinformatics: 8th International Workshop, by Eric Tannier, Chunfang Zheng, David Sankoff (auth.), Keith

By Eric Tannier, Chunfang Zheng, David Sankoff (auth.), Keith A. Crandall, Jens Lagergren (eds.)

This e-book constitutes the refereed complaints of the eighth foreign Workshop on Algorithms in Bioinformatics, WABI 2008, held in Karlsruhe, Germany, in September 2008 as a part of the ALGO 2008 meeting.

The 32 revised complete papers awarded including the summary of a keynote speak have been rigorously reviewed and chosen from eighty one submissions. All present problems with algorithms in bioinformatics are addressed, achieving from mathematical instruments to experimental stories of approximation algorithms and stories on major computational analyses. the themes diversity in organic applicability from genome mapping, to series meeting, to microarray caliber, to phylogenetic inference, to molecular modeling.

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Additional info for Algorithms in Bioinformatics: 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings

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Zhang, W. Arndt, and J. Tang Genomes Doubled Genomes A={‹ -5, 1, 6, 3 ›, ‹ 2, 4 ›} B={‹ 1, 6 ›, ‹ -5, -4, -3, -2 ›} A={‹ 10, 9, 1, 2, 11, 12, 5, 6 ›, B ={‹ 1, 2, 11, 12 ›, ‹ 3, 4, 7, 8 ›} Canonical Chromosome Ordering ‹ 10, 9, 8, 7, 6, 5, 4, 3 ›} 2 4 -3 -6 -1 5 162345 G(A,B) 10 AG(A,B) 9 1 2 {5} {-5,-1} {-1} {1,-6} 11 12 {1,-6} {6,-3} {6} {5} 5 6 {3} 3 {-2} 4 7 {2,-4} {4} {-5,4} {-4,3} {-3,2} {-2} 8 Fig. 1. The G(A, B) is the capless breakpoint graph of genome A and B. In G(A, B) diamonds represent B-ends, squares represent A-ends.

Proof. Since there are 2k connecting edges, the number of cycles of size 1 must be 2k. Then the number of remaining non-0 edges is 2mNG − 2k. Hence there are mNG − k cycles of size 2. The maximum total number of cycles is mNG + k. ◦◦ ◦◦ Because of the symmetry of M , the other cycles can only be of size 2. Hence M is the only twin median graph containing the maximum number of cycles. W. Xu and D. Sankoff -3 (+5) -6 (+7) -3 (+5) -6 (+7) +4 (+6) +1 (-7) +4 (+6) +1 (-7) (a) (b) Fig. 6. The contracted twin graph (a) and contracted symmetric graph (b).

While classical, Sanger-style sequencing machines were able to sequence 500 thousand basepairs per run at a cost of over $1000 per megabase, new sequencing technologies, such as Solexa/Illumina and AB SOLiD can sequence 4 billion nucleotides in the same amount of time, at the cost of only $6 per megabase. The decreased cost and higher throughput of NGS technologies, however, are offset by both a shorter read length and a higher overall sequencing error rate. Most NGS technologies reduce the cost of sequencing by running many sequencing experiments in parallel.

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