Kikin Oleg, D'Antonio Lawrence, Bagga Paramjeet S
Bioinformatics, School of Theoretical and Applied Science, Ramapo College of New Jersey, Mahwah, NJ 07430, USA.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W676-82. doi: 10.1093/nar/gkl253.
The quadruplex structures formed by guanine-rich nucleic acid sequences have received significant attention recently because of growing evidence for their role in important biological processes and as therapeutic targets. G-quadruplex DNA has been suggested to regulate DNA replication and may control cellular proliferation. Sequences capable of forming G-quadruplexes in the RNA have been shown to play significant roles in regulation of polyadenylation and splicing events in mammalian transcripts. Whether quadruplex structure directly plays a role in regulating RNA processing requires investigation. Computational approaches to study G-quadruplexes allow detailed analysis of mammalian genomes. There are no known easily accessible user-friendly tools that can compute G-quadruplexes in the nucleotide sequences. We have developed a web-based server, QGRS Mapper, that predicts quadruplex forming G-rich sequences (QGRS) in nucleotide sequences. It is a user-friendly application that provides many options for defining and studying G-quadruplexes. It performs analysis of the user provided genomic sequences, e.g. promoter and telomeric regions, as well as RNA sequences. It is also useful for predicting G-quadruplex structures in oligonucleotides. The program provides options to search and retrieve desired gene/nucleotide sequence entries from NCBI databases for mapping G-quadruplexes in the context of RNA processing sites. This feature is very useful for investigating the functional relevance of G-quadruplex structure, in particular its role in regulating the gene expression by alternative processing. In addition to providing data on composition and locations of QGRS relative to the processing sites in the pre-mRNA sequence, QGRS Mapper features interactive graphic representation of the data. The user can also use the graphics module to visualize QGRS distribution patterns among all the alternative RNA products of a gene simultaneously on a single screen. QGRS Mapper can be accessed at http://bioinformatics.ramapo.edu/QGRS/.
富含鸟嘌呤的核酸序列形成的四链体结构最近受到了广泛关注，因为越来越多的证据表明它们在重要的生物学过程中发挥作用，并可作为治疗靶点。有人提出G-四链体DNA可调节DNA复制，并可能控制细胞增殖。已证明能够在RNA中形成G-四链体的序列在哺乳动物转录本的聚腺苷酸化和剪接事件调节中发挥重要作用。四链体结构是否直接参与调节RNA加工尚需研究。研究G-四链体的计算方法可对哺乳动物基因组进行详细分析。目前还没有已知的易于访问且用户友好的工具能够计算核苷酸序列中的G-四链体。我们开发了一个基于网络的服务器QGRS Mapper，它可以预测核苷酸序列中形成四链体的富含G的序列（QGRS）。这是一个用户友好的应用程序，提供了许多定义和研究G-四链体的选项。它可以对用户提供的基因组序列（如启动子和端粒区域）以及RNA序列进行分析。它也可用于预测寡核苷酸中的G-四链体结构。该程序提供了从NCBI数据库中搜索和检索所需基因/核苷酸序列条目的选项，以便在RNA加工位点的背景下绘制G-四链体图谱。此功能对于研究G-四链体结构的功能相关性非常有用，特别是其在通过可变加工调节基因表达中的作用。除了提供QGRS相对于前体mRNA序列加工位点的组成和位置数据外，QGRS Mapper还具有数据的交互式图形表示功能。用户还可以使用图形模块在单个屏幕上同时可视化基因所有可变RNA产物之间的QGRS分布模式。可通过http://bioinformatics.ramapo.edu/QGRS/访问QGRS Mapper。
Zotero 插件
