An efficient algorithm for the identification of repetitive variable motifs in the regulatory sequences of co-expressed genes

Authors:
Abanish Singh;Nikola Stojanovic
Affiliations:
Department of Computer Science and Engineering, The University of Texas at Arlington, Arlington, TX;Department of Computer Science and Engineering, The University of Texas at Arlington, Arlington, TX
Venue:
ISCIS'06 Proceedings of the 21st international conference on Computer and Information Sciences
Year:
2006

Citing 3
Cited 1

Metrics for comparing regulatory sequences on the basis of pattern counts

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BEST: Binding-site Estimation Suite of Tools

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A study of the repetitive structure and distribution of short motifs in human genomic sequences

International Journal of Bioinformatics Research and Applications

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Abstract

Over the last several years there has been an explosion in the number of computational methods for the detection of transcription factor binding sites in DNA sequences. Although there has been some success in this field, the existing tools are still neither sensitive nor specific enough, usually suffering from the detection of a large number of false positive signals. Given the properties of genomic sequences this is not unexpected, but one can still find interesting features worthy of further computational and laboratory bench study. We present an efficient algorithm developed to find all significant variable motifs in given sequences. In our view, it is important that we generate complete data, upon which separate selection criteria can be applied depending on the nature of the sites one wants to locate, and their biological properties. We discuss our algorithm and our supplementary software, and conclude with an illustration of their application on two eukaryotic data sets.