COTRASIF: conservation-aided transcription-factor-binding site finder.
Nucleic Acids Res
; 37(7): e49, 2009 Apr.
Article
em En
| MEDLINE
| ID: mdl-19264796
ABSTRACT
COTRASIF is a web-based tool for the genome-wide search of evolutionary conserved regulatory regions (transcription factor-binding sites, TFBS) in eukaryotic gene promoters. Predictions are made using either a position-weight matrix search method, or a hidden Markov model search method, depending on the availability of the matrix and actual sequences of the target TFBS. COTRASIF is a fully integrated solution incorporating both a gene promoter database (based on the regular Ensembl genome annotation releases) and both JASPAR and TRANSFAC databases of TFBS matrices. To decrease the false-positives rate an integrated evolutionary conservation filter is available, which allows the selection of only those of the predicted TFBS that are present in the promoters of the related species' orthologous genes. COTRASIF is very easy to use, implements a regularly updated database of promoters and is a powerful solution for genome-wide TFBS searching. COTRASIF is freely available at http//biomed.org.ua/COTRASIF/.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Fatores de Transcrição
/
Software
/
Regiões Promotoras Genéticas
Tipo de estudo:
Health_economic_evaluation
/
Prognostic_studies
Limite:
Animals
Idioma:
En
Ano de publicação:
2009
Tipo de documento:
Article