By Jean-Philippe Doyon, Cedric Chauve, Sylvie Hamel (auth.), Craig E. Nelson, Stéphane Vialette (eds.)
This booklet constitutes the refereed complaints 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 offered have been conscientiously reviewed and chosen from forty eight preliminary submissions. The papers illustrate the the most important function of comparative genomics in figuring out genome functionality and handle a wide 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 methods to unraveling the structural evolution of genomes.
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For each side we counted the number of collinear neighbors for each gene which were orthologous. Orthology between these neighbors was defined by reciprocal BLASTP scores, requiring a minimum score of 50 and sequence identity of 80%. In order to be locally syntenic, two genes must have at least two collinear orthologous neighbors in total or one orthologous neighbor on each side. ; orthologous introns are introns in two genes whose positions in the protein alignment are within a certain number of residues [30].
3, e314 (2005) 9. : Human Line Retrotransposons Generate Processed Pseudogenes. Nat. Genet. 24, 363–367 (2000) 10. : Transcribed Processed Pseudogenes in the Human Genome: an Intermediate Form of Expressed Retrosequence Lacking Protein-coding Ability. Nucleic Acids Res. 33, 2374–2383 (2005) 11. : Evolutionary Fate of Retroposed Gene Copies in the Human Genome. Proc. Natl. Acad. Sci. U S A 103, 3220–3225 (2006) 12. : Pseudogene-derived Small Interfering RNAs Regulate Gene Expression in Mouse Oocytes.
Melanogaster protein in the far 5’ or 3’ ends of the gene. For all of these cases the query gene is much shorter than the D. melanogaster gene it is aligned to. melanogaster protein that resides more than 10,000 bases upstream of the second exon. We suspect that these are misannotations in the other Drosophila species, where the de novo gene prediction program has predicted short exons at either end of long genes as separate genes. It is possible that a gene fusion event has occurred along the D.