Use of a Drosophila genome-wide conserved sequence database to identify functionally related cis-regulatory enhancers.

ABSTRACT:

Background

Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs.

Results

We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matche

SUBMITTER: Brody T 

PROVIDER: S-EPMC3243966 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature