Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting

AUTOR(ES)

Blanchette, Mathieu

FONTE

Cold Spring Harbor Laboratory Press

RESUMO

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known.

Documentos Relacionados

• Of mice and men: phylogenetic footprinting aids the discovery of regulatory elements
• CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic Footprinting
• Regulatory Elements of the Floral Homeotic Gene AGAMOUS Identified by Phylogenetic Footprinting and ShadowingW⃞
• Computational method for discovery of estrogen responsive genes
• FootPrinter: a program designed for phylogenetic footprinting