Genome rearrangements with indels in intergenes restrict the scenario space.
BMC Bioinformatics
; 17(Suppl 14): 426, 2016 Nov 11.
Article
em En
| MEDLINE
| ID: mdl-28185582
ABSTRACT
BACKGROUND:
Given two genomes that have diverged by a series of rearrangements, we infer minimum Double Cut-and-Join (DCJ) scenarios to explain their organization differences, coupled with indel scenarios to explain their intergene size distribution, where DCJs themselves also alter the sizes of broken intergenes.RESULTS:
We give a polynomial-time algorithm that, given two genomes with arbitrary intergene size distributions, outputs a DCJ scenario which optimizes on the number of DCJs, and given this optimal number of DCJs, optimizes on the total sum of the sizes of the indels.CONCLUSIONS:
We show that there is a valuable information in the intergene sizes concerning the rearrangement scenario itself. On simulated data we show that statistical properties of the inferred scenarios are closer to the true ones than DCJ only scenarios, i.e. scenarios which do not handle intergene sizes.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Rearranjo Gênico
/
Genoma
/
Modelos Genéticos
Idioma:
En
Revista:
BMC Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2016
Tipo de documento:
Article
País de afiliação:
França