Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
BMC Bioinformatics. 2011 Aug 3;12:317. doi: 10.1186/1471-2105-12-317.
Nucleolar localization sequences (NoLSs) are short targeting sequences responsible for the localization of proteins to the nucleolus. Given the large number of proteins experimentally detected in the nucleolus and the central role of this subnuclear compartment in the cell, NoLSs are likely to be important regulatory elements controlling cellular traffic. Although many proteins have been reported to contain NoLSs, the systematic characterization of this group of targeting motifs has only recently been carried out.
Here, we describe NoD, a web server and a command line program that predicts the presence of NoLSs in proteins. Using the web server, users can submit protein sequences through the NoD input form and are provided with a graphical output of the NoLS score as a function of protein position. While the web server is most convenient for making prediction for just a few proteins, the command line version of NoD can return predictions for complete proteomes. NoD is based on our recently described human-trained artificial neural network predictor. Through stringent independent testing of the predictor using available experimentally validated NoLS-containing eukaryotic and viral proteins, the NoD sensitivity and positive predictive value were estimated to be 71% and 79% respectively.
NoD is the first tool to provide predictions of nucleolar localization sequences in diverse eukaryotes and viruses. NoD can be run interactively online at http://www.compbio.dundee.ac.uk/nod or downloaded to use locally.
核仁定位序列（NoLSs）是负责将蛋白质定位到核仁的短靶向序列。鉴于在核仁中实验检测到的大量蛋白质以及该亚核区室在细胞中的核心作用，NoLSs 很可能是控制细胞运输的重要调节元件。尽管已经报道了许多蛋白质含有 NoLSs，但对这组靶向基序的系统特征描述直到最近才进行。
在这里，我们描述了 NoD，这是一个网络服务器和一个命令行程序，用于预测蛋白质中 NoLSs 的存在。使用网络服务器，用户可以通过 NoD 输入表单提交蛋白质序列，并获得 NoLS 分数作为蛋白质位置函数的图形输出。虽然网络服务器最适合对少数几个蛋白质进行预测，但 NoD 的命令行版本可以返回完整蛋白质组的预测结果。NoD 是基于我们最近描述的经过人类训练的人工神经网络预测器。通过使用现有的经过实验验证的含有 NoLS 的真核生物和病毒蛋白质对预测器进行严格的独立测试，估计 NoD 的灵敏度和阳性预测值分别为 71%和 79%。
NoD 是第一个提供在不同真核生物和病毒中核仁定位序列预测的工具。NoD 可以在 http://www.compbio.dundee.ac.uk/nod 上在线交互运行，也可以下载到本地使用。
