By Max A. Alekseyev (auth.), Glenn Tesler, Dannie Durand (eds.)
This publication constitutes the refereed court cases of the fifth RECOMB Comparative Genomics satellite tv for pc Workshop, RECOMB-CG 2007, held in San Diego, CA, united states, in September 2007.
The 14 revised complete papers offered have been conscientiously reviewed and chosen from 18 preliminary submissions. The papers tackle a huge number of points and parts of the sphere of comparative genomics, starting from quantitative discoveries approximately genome constitution to algorithms for comparative inference to theorems at the complexity of computational difficulties required for genome comparison.
Read Online or Download Comparative Genomics: RECOMB 2007 International Workshop, RECOMB-CG 2007, San Diego, CA, USA, September 16-18, 2007. Proceedings PDF
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Additional info for Comparative Genomics: RECOMB 2007 International Workshop, RECOMB-CG 2007, San Diego, CA, USA, September 16-18, 2007. Proceedings
Let G be the genome with signed ordering of g1 , g2 , · · · , gn . An inversion between indices i and j (i ≤ j), transforms G to a new genome with linear ordering g1 , g2 , · · · , gi−1 , −g j , −g j−1, · · · , −gi , g j+1 , · · · , gn A transposition on genome G acts on three indices i, j, k, with i ≤ j and k ∈ / [i, j], picking up the interval gi , gi+1 , · · · , g j and inserting it immediately after gk . Thus genome G is replaced by (assume k > j): g1 , · · · , gi−1 , g j+1 , · · · , gk , gi , gi+1 , · · · , g j , gk+1 , · · · , gn An transversion is a transposition followed by an inversion of the transposed subsequence; it is also called an inverted transposition.
This condensation procedure is very effective when the genomes are close: a median of genomes with 1, 000 genes and 50 inversions per edge can be condensed to ∼ 200 genes only. In practice, given the smallest edge length e and number of genes n, we found the ratio ne is a good indicator about the difficulty of inversion median problem. Siepel’s median solver cannot handle datasets with ne > 15%, and its search approach limits it to small genomes (< 100 genes) as well. On the other hand, Caprara’s median solver will be able to handle datasets with 1, 000 genes for ne ≤ 20%.
First, the choice of the start permutation has some impact and our experiments show that using the permutation nearest to the center produces the best median scores. Second, despite our efforts to prevent redundant computation, a very large amount still occurs and we used a permutation hash table to check for redundant search paths. This is not a critical aspect and can be removed with little impact–in fact, due to memory constraints it must be removed for genomes larger than approximately 400 genes.