By Jean-Philippe Doyon, Cedric Chauve, Sylvie Hamel (auth.), Craig E. Nelson, Stéphane Vialette (eds.)
This booklet constitutes the refereed court cases of the sixth RECOMB Comparative Genomics satellite tv for pc Workshop, RECOMB-CG 2008, held in Paris, France, in October 2008.
The 19 revised complete papers awarded have been conscientiously reviewed and chosen from forty eight preliminary submissions. The papers illustrate the an important position of comparative genomics in figuring out genome functionality and deal with a extensive number of facets, starting from the inference of evolution in genetic regulatory networks to the divergent fates of gene and genome duplication occasions and to the significance of latest computational ways to unraveling the structural evolution of genomes.
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Additional info for Comparative Genomics: International Workshop, RECOMB-CG 2008, Paris, France, October 13-15, 2008. Proceedings
Whole genome duplication has been important to the evolution of many lineages , but it is a relatively rare event. Unlike whole genome duplication events, segmental duplications occur continuously and have contributed significantly to the divergence of gene content between mammalian genomes. Duplication by retrotransposition also occurs quite frequently, but because these new retrotransposed gene copies lack the ﬂanking regulatory material of the parental gene, they have long been believed to give rise primarily to non-functional pseudogenes [16,25].
After this analysis, for every pair (gi , gj ) of family members we obtained two ij numbers 0 ≤ nij u , nd ≤ 3 representing the homology upstream and downstream neighbors. , whenever ij nij u , nd ≥ 1). , when nij u + nd ≤ 1) we assigned a synteny level si,j of 0. Local synteny levels were used in a two-stage clustering algorithm (see Algorithm 1) to identify syntenic ortholog/paralog clusters. In our algorithm, for a set X of genes and pseudogenes, Sp(X) denotes the set of species represented in X.
Gene duplication has long been recognized as a major force in genome evolution and has recently been recognized as an important source of individual variation. For many years the origin of functional gene duplicates was assumed to be whole or partial genome duplication events, but recently retrotransposition has also been shown to contribute new functional protein coding genes and siRNA’s. Here we present a method for the identiﬁcation and classiﬁcation of retrotransposed and segmentally duplicated genes and pseudogenes based on local synteny.
Comparative Genomics: International Workshop, RECOMB-CG 2008, Paris, France, October 13-15, 2008. Proceedings by Jean-Philippe Doyon, Cedric Chauve, Sylvie Hamel (auth.), Craig E. Nelson, Stéphane Vialette (eds.)