Searching for non-B DNA-forming motifs using nBMST (non-B DNA Motif Search Tool)

摘要

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 Aphased repeats (static bending). Basic protocol 1 illustrates different ways of submitting sequences, the required file input format, results comprising downloadable Generic Feature Format (GFF) files, static Portable Network Graphics (PNG) images, dynamic PolyBrowse link, and accessing documentation through the Help and Frequently Asked Questions (FAQs) pages. Basic Protocol 2 illustrates a brief overview of some of the PolyBrowse functionalities, particularly with reference to possible associations between predicted non-B DNA forming motifs and disease causing effects. 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 20 megabytes (MB).