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

doi:10.1002/0471142905.hg1807s73

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

Institute for Health Informatics

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27 Scopus citations

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 language	English (US)
Article number	18.7
Journal	Current Protocols in Human Genetics
Issue number	SUPPL.73
DOIs	https://doi.org/10.1002/0471142905.hg1807s73
State	Published - Apr 2012

Keywords

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

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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.",

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

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AU - Cer, R. Z.

AU - Bruce, K. H.

AU - Donohue, D. E.

AU - Temiz, N. A.

AU - Mudunuri, U. S.

AU - Yi, M.

AU - Volfovsky, N.

AU - Bacolla, A.

AU - Luke, B. T.

AU - Collins, J. R.

AU - Stephens, R. M.

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AB - 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.

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KW - Tandem repeats

KW - Triplex

KW - Z-DNA

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

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