Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome

Background: This paper addresses the problem of recognising DNA cis-regulatory modules which are located far from genes. Experimental procedures for this are slow and costly, and computational methods are hard, because they lack positional information. Results: We present a novel statistical method, the "fluffy-tail test", to recognise regulatory DNA. We exploit one of the basic informational properties of regulatory DNA: abundance of overrepresented transcription factor binding site (TFBS) motifs, although we do not look for specific TFBS motifs, per se . Though overrepresentation of TFBS motifs in regulatory DNA has been intensively exploited by many algorithms, it is still a difficult problem to distinguish regulatory from other genomic DNA. Conclusion: We show that, in the data used, our method is able to distinguish cis-regulatory modules by exploiting statistical differences between the probability distributions of similar words in regulatory and other DNA. The potenti...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Irina I. Abnizova, Rene te Boekhorst, Klaudia Walter, Walter R. Gilks
• Keywords: BMCBI 2005, Regulatory, Regulatory Dna, Transcription Factor