Key result
The non-B DNA Motif Search Tool (nBMST) is a versatile, web-based resource that allows users to search for sequence motifs predicted to form alternative DNA conformations up to 20 Mbp.
Provides a protocol for using the nBMST web-based resource to identify non-B DNA motifs in genomic sequences.
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Supports genomic motif analysis in research settings; leaves open clinical translation pending validation.
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).
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Cer et al. (2012) studied this question. nBMST (Non-B DNA Motif Search Tool) was evaluated. The non-B DNA Motif Search Tool (nBMST) is a versatile, web-based resource that allows users to search for sequence motifs predicted to form alternative DNA conformations up to 20 Mbp.
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