Evolutionary simulations to detect functional lineage-specific genes.

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Serval ID
serval:BIB_43D3835CBB98
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Evolutionary simulations to detect functional lineage-specific genes.
Journal
Bioinformatics
Author(s)
Dupanloup I., Kaessmann H.
ISSN
1460-2059[electronic]
Publication state
Published
Issued date
2006
Peer-reviewed
Oui
Volume
22
Number
15
Pages
1815-1822
Language
english
Abstract
MOTIVATION: Supporting the functionality of recent duplicate gene copies is usually difficult, owing to high sequence similarity between duplicate counterparts and shallow phylogenies, which hamper both the statistical and experimental inference. RESULTS: We developed an integrated evolutionary approach to identify functional duplicate gene copies and other lineage-specific genes. By repeatedly simulating neutral evolution, our method estimates the probability that an ORF was selectively conserved and is therefore likely to represent a bona fide coding region. In parallel, our method tests whether the accumulation of non-synonymous substitutions reveals signatures of selective constraint. We show that our approach has high power to identify functional lineage-specific genes using simulated and real data. For example, a coding region of average length (approximately 1400 bp), restricted to hominoids, can be predicted to be functional in approximately 94-100% of cases. Notably, the method may support functionality for instances where classical selection tests based on the ratio of non-synonymous to synonymous substitutions fail to reveal signatures of selection. Our method is available as an automated tool, ReEVOLVER, which will also be useful to systematically detect functional lineage-specific genes of closely related species on a large scale. AVAILABILITY: ReEVOLVER is available at http://www.unil.ch/cig/page7858.html.
Keywords
Animals, Base Sequence, Cell Lineage, Chromosome Mapping, Conserved Sequence, DNA Mutational Analysis, Evolution, Molecular, Hominidae, Humans, Linkage Disequilibrium, Molecular Sequence Data, Open Reading Frames, Phylogeny, Sequence Alignment, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
Pubmed
Web of science
Open Access
Yes
Create date
24/01/2008 16:41
Last modification date
25/09/2019 7:09
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