Unit

UNIT 18.7 Searching for Non-B DNA-Forming Motifs Using nBMST (Non-B DNA Motif Search Tool)

  1. R.Z. Cer1,
  2. K.H. Bruce1,
  3. D.E. Donohue1,
  4. N.A. Temiz1,
  5. U.S. Mudunuri1,
  6. M. Yi1,
  7. N. Volfovsky1,
  8. A. Bacolla1,2,
  9. B.T. Luke1,
  10. J.R. Collins1,
  11. R.M. Stephens1

Published Online: 1 APR 2012

DOI: 10.1002/0471142905.hg1807s73

Current Protocols in Human Genetics

Current Protocols in Human Genetics

How to Cite

Cer, R., Bruce, K., Donohue, D., Temiz, N., Mudunuri, U., Yi, M., Volfovsky, N., Bacolla, A., Luke, B., Collins, J. and Stephens, R. 2012. Searching for Non-B DNA-Forming Motifs Using nBMST (Non-B DNA Motif Search Tool). Current Protocols in Human Genetics. 73:18.7:18.7.1–18.7.22.

Author Information

  1. 1

    Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, Maryland

  2. 2

    The Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, The University of Texas at Austin, Austin, Texas

Publication History

  1. Published Online: 1 APR 2012
  2. Published Print: APR 2012

Abstract

This unit describes basic protocols on using the non-B DNA Motif Search Tool (nBMST) to search for sequence motifs predicted to form alternative DNA conformations that differ from the canonical right-handed Watson-Crick double-helix, collectively known as non-B DNA, and on using the associated PolyBrowse, a GBrowse–based genomic browser. The nBMST is a Web-based resource that allows users to submit one or more DNA sequences to search for inverted repeats (cruciform DNA), mirror repeats (triplex DNA), direct/tandem repeats (slipped/hairpin structures), G4 motifs (tetraplex, G-quadruplex DNA), alternating purine-pyrimidine tracts (left-handed Z-DNA), and A-phased repeats (static bending). The nBMST is versatile, simple to use, does not require bioinformatics skills, and can be applied to any type of DNA sequences, including viral and bacterial genomes, up to an aggregate of 20 megabasepairs (Mbp). Curr. Protoc. Hum. Genet. 73:18.7.1-18.7.22. © 2012 by John Wiley & Sons, Inc.

Keywords:

  • nBMST;
  • non-B DNA;
  • nucleotide sequence analysis;
  • G-quadruplex;
  • triplex;
  • cruciform;
  • Z-DNA;
  • hairpin;
  • slipped DNA;
  • alternative DNA structure;
  • tandem repeats;
  • PolyBrowse