Searching for Non-B DNA-forming Motifs Using NBMST (non-B DNA Motif Search Tool)

Overview

Journal Curr Protoc Hum Genet

Specialty Genetics

Date 2012 Apr 4

PMID 22470144

Citations 17

Authors

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

Affiliations

Soon will be listed here.

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).

Citing Articles

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