Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.

ABSTRACT:

Background

Regulation of gene transcription is crucial for the function and development of all organisms. While gene prediction programs that identify protein coding sequence are used with remarkable success in the annotation of genomes, the development of computational methods to analyze noncoding regions and to delineate transcriptional control elements is still in its infancy.

Results

Here we present novel algorithms to detect cis-regulatory modules through genome wide scans for clusters of transcription factor binding sites using three levels of prior information. When binding sites for the factors are known, our statistical segmentation algorithm, Ahab, yields about 150 putative gap gene regulated modules, with no adjustable parameters other than a window size. If one o

SUBMITTER: Rajewsky N 

PROVIDER: S-EPMC139975 | biostudies-literature | 2002 Oct

REPOSITORIES: biostudies-literature