PhyloScan: identification of transcription factor binding sites using cross-species evidence.

ABSTRACT:

Background

When transcription factor binding sites are known for a particular transcription factor, it is possible to construct a motif model that can be used to scan sequences for additional sites. However, few statistically significant sites are revealed when a transcription factor binding site motif model is used to scan a genome-scale database.

Methods

We have developed a scanning algorithm, PhyloScan, which combines evidence from matching sites found in orthologous data from several related species with evidence from multiple sites within an intergenic region, to better detect regulons. The orthologous sequence data may be multiply aligned, unaligned, or a combination of aligned and unaligned. In aligned data, PhyloScan statistically accounts for the phylogenetic depend

SUBMITTER: Carmack CS 

PROVIDER: S-EPMC1794230 | biostudies-literature | 2007 Jan

REPOSITORIES: biostudies-literature