DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding.

Journal: Bioinformatics (Oxford, England)
Published Date: Oct 1, 2017

Abstract

MOTIVATION: Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs, etc. Several methods have been developed to jointly account for DNA sequence and shape properties in predicting TF binding affinity. However, a limitation of these methods is that they typically require a training set of aligned TF binding sites.

Authors

  • Wenxiu Ma
    Department of Statistics, University of California Riverside, Riverside, CA 92521, USA.
  • Lin Yang
    National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China.
  • Remo Rohs
    Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, CA 90089, USA.
  • William Stafford Noble
    1] Department of Computer Science and Engineering, University of Washington, 185 Stevens Way, Seattle, Washington 98195-2350, USA. [2] Department of Genome Sciences, University of Washington, 3720 15th Ave NE Seattle, Washington 98195-5065, USA.

Keywords

External Resources

Popular Topics
Recent Journals