Evolutionary simulations to detect functional lineage-specific genes.
Bioinformatics
; 22(15): 1815-22, 2006 Aug 01.
Article
em En
| MEDLINE
| ID: mdl-16766551
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.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Hominidae
/
Desequilíbrio de Ligação
/
Fases de Leitura Aberta
/
Mapeamento Cromossômico
/
Análise de Sequência de DNA
/
Evolução Molecular
/
Linhagem da Célula
Limite:
Animals
/
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2006
Tipo de documento:
Article
País de afiliação:
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