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An Efficient Algorithm for the Identification of Repetitive Variable Motifs in the Regulatory Sequences of Co-expressed Genes

  • Abanish Singh
  • Nikola Stojanovic
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4263)

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.

Keywords

Transcription Factor Binding Site Upstream Sequence Mixed Lineage Leukemia Variable Motif Positional Conservation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Abanish Singh
    • 1
  • Nikola Stojanovic
    • 1
  1. 1.Department of Computer Science and EngineeringThe University of Texas at ArlingtonArlingtonUSA

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