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Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test.

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Abnizova, Irina 
te Boekhorst, Rene 
Walter, Klaudia 
Gilks, Walter R 


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 over-represented 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 potential application of our method includes annotation of new genomic sequences and motif discovery.



Algorithms, Amino Acid Motifs, Animals, Base Sequence, Binding Sites, Cell Nucleus, Chromatin, Cluster Analysis, Computational Biology, DNA, Databases, Genetic, Drosophila melanogaster, Genes, Insect, Genes, Regulator, Genome, Genomics, Models, Statistical, Molecular Sequence Data, Sequence Analysis, DNA, Transcription, Genetic

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BMC Bioinformatics

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Springer Science and Business Media LLC