REEF: searching REgionally Enriched Features in genomes.

ABSTRACT:

Background

In Eukaryotic genomes, different features including genes are not uniformly distributed. The integration of annotation information and genomic position of functional DNA elements in the Eukaryotic genomes opened the way to test novel hypotheses of higher order genome organization and regulation of expression.

Results

REEF is a new tool, aimed at identifying genomic regions enriched in specific features, such as a class or group of genes homogeneous for expression and/or functional characteristics. The method for the calculation of local feature enrichment uses test statistic based on the Hypergeometric Distribution applied genome-wide by using a sliding window approach and adopting the False Discovery Rate for controlling multiplicity. REEF software, source code a

SUBMITTER: Coppe A 

PROVIDER: S-EPMC1624853 | biostudies-literature | 2006 Oct

REPOSITORIES: biostudies-literature