REEF: searching REgionally Enriched Features in genomes

被引:31
作者
Coppe, Alessandro [1 ]
Danieli, Gian Antonio [1 ]
Bortoluzzi, Stefania [1 ]
机构
[1] Univ Padua, Dept Biol, I-35131 Padua, Italy
关键词
D O I
10.1186/1471-2105-7-453
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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/. Conclusion: REEF can aid to shed light on the role of organization of specific genomic regions in the determination of their functional role.
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页数:7
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