Software

REEF: searching REgionally Enriched Features in genomes

Alessandro Coppe, Gian Antonio Danieli and Stefania Bortoluzzi^*

• * Corresponding author: Stefania Bortoluzzi stefibo@bio.unipd.it

Author Affiliations

Department of Biology, University of Padova, via G. Colombo 3, 35131, Padova, Italy

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BMC Bioinformatics 2006, 7:453 doi:10.1186/1471-2105-7-453

Published: 16 October 2006

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 and documentation are freely available at http://telethon.bio.unipd.it/bioinfo/reef/ webcite.

Conclusion

REEF can aid to shed light on the role of organization of specific genomic regions in the determination of their functional role.