Alignment-free estimation of nucleotide diversity.
Bioinformatics
; 27(4): 449-55, 2011 Feb 15.
Article
em En
| MEDLINE
| ID: mdl-21156730
ABSTRACT
MOTIVATION Sequencing capacity is currently growing more rapidly than CPU speed, leading to an analysis bottleneck in many genome projects. Alignment-free sequence analysis methods tend to be more efficient than their alignment-based counterparts. They may, therefore, be important in the long run for keeping sequence analysis abreast with sequencing. RESULTS:
We derive and implement an alignment-free estimator of the number of pairwise mismatches, . Our implementation of , pim, is based on an enhanced suffix array and inherits the superior time and memory efficiency of this data structure. Simulations demonstrate that is accurate if mutations are distributed randomly along the chromosome. While real data often deviates from this ideal, remains useful for identifying regions of low genetic diversity using a sliding window approach. We demonstrate this by applying it to the complete genomes of 37 strains of Drosophila melanogaster, and to the genomes of two closely related Drosophila species, D.simulans and D.sechellia. In both cases, we detect the diversity minimum and discuss its biological implications.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Variação Genética
/
Análise de Sequência de DNA
/
Biologia Computacional
Limite:
Animals
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2011
Tipo de documento:
Article
País de afiliação:
Alemanha