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

Conference Paper

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. © Springer-Verlag Berlin Heidelberg 2006.

Full Text

Duke Authors

Cited Authors

  • Singh, A; Stojanovic, N

Published Date

  • January 1, 2006

Published In

Volume / Issue

  • 4263 LNCS /

Start / End Page

  • 182 - 191

Electronic International Standard Serial Number (EISSN)

  • 1611-3349

International Standard Serial Number (ISSN)

  • 0302-9743

International Standard Book Number 10 (ISBN-10)

  • 3540472428

International Standard Book Number 13 (ISBN-13)

  • 9783540472421

Digital Object Identifier (DOI)

  • 10.1007/11902140_21

Citation Source

  • Scopus