Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool).
Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool).
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DOI：
10.1002/0471142905.hg1807s73
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发表时间：
2012-04
影响因子：
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通讯作者：
Stephens, R M
中科院分区：
文献类型：
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作者：
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
本单元描述了使用非B DNA基序搜索工具（nBMST）搜索预测形成不同于典型右手沃森-克里克双螺旋的替代DNA构象的序列基序（统称为非B DNA）的基本协议，以及使用相关的PolyBrowse（基于GBrowse的基因组浏览器）。nBMST是一个基于网络的资源，允许用户提交一个或多个DNA序列来搜索反向重复序列（十字形DNA），镜像重复序列（三链DNA），直接/串联重复序列（滑动/发夹结构），G4基序（四链体，G-quadruplex DNA），交替嘌呤-嘧啶束（左手Z-DNA）和非相位重复序列（静态弯曲）。基本协议1说明了提交序列、所需文件输入格式、包括可下载通用特征格式（GFF）文件的结果、静态可移植网络图形（PNG）图像、动态PolyBrowse链接以及通过帮助和常见问题（FAQ）页面访问文档的不同方式。基本方案2简要概述了PolyBrowse的一些功能，特别是关于预测的非B DNA形成基序和致病效应之间的可能关联。nBMST用途广泛，使用简单，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，高达20 MB。
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 Aphased repeats (static bending). Basic protocol 1 illustrates different ways of submitting sequences, the required file input format, results comprising downloadable Generic Feature Format (GFF) files, static Portable Network Graphics (PNG) images, dynamic PolyBrowse link, and accessing documentation through the Help and Frequently Asked Questions (FAQs) pages. Basic Protocol 2 illustrates a brief overview of some of the PolyBrowse functionalities, particularly with reference to possible associations between predicted non-B DNA forming motifs and disease causing effects. 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 20 megabytes (MB).