Searching for Non‐B DNA‐Forming Motifs Using nBMST (Non‐B DNA Motif Search Tool)
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 PolyB...
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| Veröffentlicht in: | Current Protocols in Human Genetics 2012-04, Vol.73 (1), p.18.7.1-18.7.22 |
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| creator | Cer, R.Z. Bruce, K.H. Donohue, D.E. Temiz, N.A. Mudunuri, U.S. Yi, M. Volfovsky, N. Bacolla, A. Luke, B.T. Collins, J.R. Stephens, R.M. |
| description | 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). Curr. Protoc. Hum. Genet. 73:18.7.1‐18.7.22. © 2012 by John Wiley & Sons, Inc. |
| doi_str_mv | 10.1002/0471142905.hg1807s73 |
| format | Article |
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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. 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Genet. 73:18.7.1‐18.7.22. © 2012 by John Wiley & Sons, Inc.</description><subject>alternative DNA structure</subject><subject>Animals</subject><subject>Computational Biology - methods</subject><subject>cruciform</subject><subject>Databases, Nucleic Acid</subject><subject>DNA - chemistry</subject><subject>G‐quadruplex</subject><subject>hairpin</subject><subject>Humans</subject><subject>Internet</subject><subject>nBMST</subject><subject>non‐B DNA</subject><subject>Nucleic Acid Conformation</subject><subject>Nucleotide Motifs</subject><subject>nucleotide sequence analysis</subject><subject>PolyBrowse</subject><subject>Search Engine</subject><subject>slipped DNA</subject><subject>tandem repeats</subject><subject>triplex</subject><subject>Z‐DNA</subject><issn>1934-8266</issn><issn>1934-8258</issn><issn>1934-8258</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2012</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkU1OwzAQhS0EolXhBghlByxS_BfHZoEEhQJSC0gUtpbjOG2kJC52C-qOI3BGTkKqlFJ2LEYz1nvzeaQHwAGCXQQhPoU0RohiAaPuZIw4jH1MtkAbCUJDjiO-vZ4Za4F97_MEoogLxhnZBS2MaQwRpW3w8mSU05O8GgeZdcG9rb4-Pi-Dq_uLuvetK5fK0M7yzAfPfvmoLodPo-B4w9noQUMKRtYWJ3tgJ1OFN_ur3gHP_etR7zYcPNzc9S4GoaZExCGOoSFCqIRRAyOjjcIqzbI05lAYnSUqw5yJugxLVQJTjYjiaRJzk2gmOCQdcN5wp_OkNKk21cypQk5dXiq3kFbl8q9S5RM5tm-SkAhyhGvA0Qrg7Ovc-Jksc69NUajK2LmXglEMiYhQ7aSNUzvrvTPZ-hcE5TIU-RuKXIdSrx1uXrhe-omgNpw1hve8MIt_QWXv8fZmOZNv9uGb3w</recordid><startdate>201204</startdate><enddate>201204</enddate><creator>Cer, R.Z.</creator><creator>Bruce, K.H.</creator><creator>Donohue, D.E.</creator><creator>Temiz, N.A.</creator><creator>Mudunuri, U.S.</creator><creator>Yi, M.</creator><creator>Volfovsky, N.</creator><creator>Bacolla, A.</creator><creator>Luke, B.T.</creator><creator>Collins, J.R.</creator><creator>Stephens, R.M.</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>201204</creationdate><title>Searching for Non‐B DNA‐Forming Motifs Using nBMST (Non‐B DNA Motif Search Tool)</title><author>Cer, R.Z. ; 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| issn | 1934-8266 1934-8258 1934-8258 |
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| source | MEDLINE; Alma/SFX Local Collection |
| subjects | alternative DNA structure Animals Computational Biology - methods cruciform Databases, Nucleic Acid DNA - chemistry G‐quadruplex hairpin Humans Internet nBMST non‐B DNA Nucleic Acid Conformation Nucleotide Motifs nucleotide sequence analysis PolyBrowse Search Engine slipped DNA tandem repeats triplex Z‐DNA |
| title | Searching for Non‐B DNA‐Forming Motifs Using nBMST (Non‐B DNA Motif Search Tool) |
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