Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool)

R. Z. Cer, K. H. Bruce, D. E. Donohue, N. A. Temiz, U. S. Mudunuri, M. Yi, N. Volfovsky, A. Bacolla, B. T. Luke, J. R. Collins, R. M. Stephens

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

This unit describes basic protocols on using the non-B DNA Motif Search Tool (nBMST) to search for sequence motifs predicted to form alternativeDNAconformations 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.

Original languageEnglish (US)
Article number18.7
JournalCurrent Protocols in Human Genetics
Issue numberSUPPL.73
DOIs
StatePublished - Apr 1 2012

Fingerprint

Nucleotide Motifs
Z-Form DNA
Cruciform DNA
G-Quadruplexes
Viverridae
Bacterial Genomes
Tandem Repeat Sequences
Viral Genome
Computational Biology
DNA

Keywords

  • Alternative DNA structure
  • Cruciform
  • G-quadruplex
  • Hairpin
  • Non-B DNA
  • Nucleotide sequence analysis
  • Polybrowse
  • Slipped DNA
  • Tandem repeats
  • Triplex
  • Z-DNA
  • nBMST

Cite this

Cer, R. Z., Bruce, K. H., Donohue, D. E., Temiz, N. A., Mudunuri, U. S., Yi, M., ... Stephens, R. M. (2012). Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool). Current Protocols in Human Genetics, (SUPPL.73), [18.7]. https://doi.org/10.1002/0471142905.hg1807s73

Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool). / Cer, R. Z.; Bruce, K. H.; Donohue, D. E.; Temiz, N. A.; Mudunuri, U. S.; Yi, M.; Volfovsky, N.; Bacolla, A.; Luke, B. T.; Collins, J. R.; Stephens, R. M.

In: Current Protocols in Human Genetics, No. SUPPL.73, 18.7, 01.04.2012.

Research output: Contribution to journalArticle

Cer, RZ, Bruce, KH, Donohue, DE, Temiz, NA, Mudunuri, US, Yi, M, Volfovsky, N, Bacolla, A, Luke, BT, Collins, JR & Stephens, RM 2012, 'Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool)', Current Protocols in Human Genetics, no. SUPPL.73, 18.7. https://doi.org/10.1002/0471142905.hg1807s73
Cer, R. Z. ; Bruce, K. H. ; Donohue, D. E. ; Temiz, N. A. ; Mudunuri, U. S. ; Yi, M. ; Volfovsky, N. ; Bacolla, A. ; Luke, B. T. ; Collins, J. R. ; Stephens, R. M. / Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool). In: Current Protocols in Human Genetics. 2012 ; No. SUPPL.73.
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