HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing.

ABSTRACT:

Background

Correct temporal and spatial gene expression during metazoan development relies on combinatorial interactions between different transcription factors. As a consequence, cis-regulatory elements often colocalize in clusters termed cis-regulatory modules. These may have requirements on organizational features such as spacing, order and helical phasing (periodic spacing) between binding sites. Due to the turning of the DNA helix, a small modification of the distance between a pair of sites may sometimes drastically disrupt function, while insertion of a full helical turn of DNA (10-11 bp) between cis elements may cause functionality to be restored. Recently, de novo motif discovery methods which incorporate organizational properties such as colocalization and order preferenc

SUBMITTER: Larsson E 

PROVIDER: S-EPMC2200674 | biostudies-literature | 2007 Oct

REPOSITORIES: biostudies-literature