Using the Gibbs Motif Sampler for phylogenetic footprinting.
Methods Mol Biol
; 395: 403-24, 2007.
Article
em En
| MEDLINE
| ID: mdl-17993688
ABSTRACT
The Gibbs Motif Sampler (Gibbs) is a software package used to predict conserved elements in biopolymer sequences. Although the software can be used to locate conserved motifs in protein sequences, its most common use is the prediction of transcription factor binding sites (TFBSs) in promoters upstream of gene sequences. We will describe approaches that use Gibbs to locate TFBSs in a collection of orthologous nucleotide sequences, i.e., phylogenetic footprinting. To illustrate this technique, we present examples that use Gibbs to detect binding sites for the transcription factor LexA in orthologous sequence data from representative species belonging to two different proteobacterial divisions.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Filogenia
/
Fatores de Transcrição
Tipo de estudo:
Prognostic_studies
Idioma:
En
Ano de publicação:
2007
Tipo de documento:
Article