使用nBMST（非B型DNA基序搜索工具）搜索形成非B型DNA的基序。
Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool).
作者信息
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
机构信息
Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc, National Cancer Institute-Frederick, Frederick, Maryland, USA.
出版信息
Curr Protoc Hum Genet. 2012 Apr;Chapter 18:Unit 18.7.1-22. doi: 10.1002/0471142905.hg1807s73.
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).
摘要
本单元介绍了使用非B型DNA基序搜索工具（nBMST）搜索预测会形成不同于经典右手沃森-克里克双螺旋结构的替代DNA构象（统称为非B型DNA）的序列基序的基本协议，以及使用相关的PolyBrowse（一种基于GBrowse的基因组浏览器）的基本协议。nBMST是一个基于网络的资源，允许用户提交一个或多个DNA序列，以搜索反向重复序列（十字形DNA）、镜像重复序列（三链体DNA）、直接/串联重复序列（滑动/发夹结构）、G4基序（四链体、G-四链体DNA）、交替嘌呤-嘧啶序列（左手Z-DNA）和A相重复序列（静态弯曲）。nBMST用途广泛，易于使用，不需要生物信息学技能，可应用于任何类型的DNA序列，包括病毒和细菌基因组，最大可达20兆碱基对（Mbp）的总和。
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