Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes.
Nucleic Acids Res
; 39(22): e150, 2011 Dec.
Article
en En
| MEDLINE
| ID: mdl-21965536
ABSTRACT
Existing methods for orthologous gene mapping suffer from two general problems (i) they are computationally too slow and their results are difficult to interpret for automated large-scale applications when based on phylogenetic analyses; or (ii) they are too prone to making mistakes in dealing with complex situations involving horizontal gene transfers and gene fusion due to the lack of a sound basis when based on sequence similarity information. We present a novel algorithm, Global Optimization Strategy (GOST), for orthologous gene mapping through combining sequence similarity and contextual (working partners) information, using a combinatorial optimization framework. Genome-scale applications of GOST show substantial improvements over the predictions by three popular sequence similarity-based orthology mapping programs. Our analysis indicates that our algorithm overcomes the intrinsic issues faced by sequence similarity-based methods, when orthology mapping involves gene fusions and horizontal gene transfers. Our program runs as efficiently as the most efficient sequence similarity-based algorithm in the public domain. GOST is freely downloadable at http//csbl.bmb.uga.edu/~maqin/GOST.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Algoritmos
/
Mapeo Cromosómico
/
Genoma Bacteriano
Tipo de estudio:
Evaluation_studies
/
Risk_factors_studies
Idioma:
En
Revista:
Nucleic Acids Res
Año:
2011
Tipo del documento:
Article
País de afiliación:
Estados Unidos