title: 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 and documentation are freely available at http://telethon.bio.unipd.it/bioinfo/reef/.
  
  
  CONCLUSIONS
  REEF can aid to shed light on the role of organization of specific genomic regions in the determination of their functional role.
authors.affiliation: Department of Biology, University of Padova, via G, Colombo 3, 35131, Padova, Italy. ale@telethon.bio.unipd.it
authors.forename: Alessandro
authors.initials: A
authors.lastname: Coppe
authors.forename: Gian Antonio
authors.initials: GA
authors.lastname: Danieli
authors.forename: Stefania
authors.initials: S
authors.lastname: Bortoluzzi
mesh_terms: D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D017124:Conserved Sequence; D008040:Genetic Linkage; D015810:Linkage Disequilibrium / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software