title: Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool).
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).
authors.affiliation: Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc, National Cancer Institute-Frederick, Frederick, Maryland, USA.
authors.forename: R Z
authors.initials: RZ
authors.lastname: Cer
authors.forename: K H
authors.initials: KH
authors.lastname: Bruce
authors.forename: D E
authors.initials: DE
authors.lastname: Donohue
authors.forename: N A
authors.initials: NA
authors.lastname: Temiz
authors.forename: U S
authors.initials: US
authors.lastname: Mudunuri
authors.forename: M
authors.initials: M
authors.lastname: Yi
authors.forename: N
authors.initials: N
authors.lastname: Volfovsky
authors.forename: A
authors.initials: A
authors.lastname: Bacolla
authors.forename: B T
authors.initials: BT
authors.lastname: Luke
authors.forename: J R
authors.initials: JR
authors.lastname: Collins
authors.forename: R M
authors.initials: RM
authors.lastname: Stephens
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D006801:Humans; D020407:Internet; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D057386:Search Engine
chemical_list: D004247:DNA