Biological sequence motif discovery using motif-x.
Biological sequence motif discovery using motif-x.
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DOI：
10.1002/0471250953.bi1316s36
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发表时间：
2011-09-01
影响因子：
--
通讯作者：
Schwartz, Daniel
中科院分区：
文献类型：
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作者：
Chou, Michael F;Schwartz, Daniel
最近大量的蛋白质组质谱数据提供了证据，表明细胞中几乎每一种蛋白质都经历了某种形式的翻译后修饰。我们描述了一个协议，使用scan-x网站，以查看预测的乙酰化位点在人类蛋白质组和预测的磷酸化位点在人类，小鼠，苍蝇，酵母蛋白质组具有高度的特异性。该工具几乎可以从任何具有Web浏览器的计算机访问。基于Web的motif-x程序提供了一个简单的界面，可以从大量的数据集中提取具有统计学意义的基序，例如MS/MS翻译后修饰数据和具有共同生物学功能的蛋白质组。用户可以在任何兼容Web的计算机上使用普通Web浏览器上传数据文件和下载结果。一旦提交，数据分析在相关的高速计算机集群上迅速进行，它们产生句法和基于图像的主题结果和统计数据。所提出的协议演示了在三个常见的用户场景中使用motif-x。
The recent plethora of proteomic mass spectrometry data is providing evidence that almost every protein in the cell undergoes some form of post-translational modification. We describe a protocol to use the scan-x Web site to view predicted acetylation sites in the human proteome and predicted phosphorylation sites in the human, mouse, fly, and yeast proteomes with high specificity. This tool is accessible from virtually any computer with a Web browser. The only requirement is a means of searching for a protein of interest in one of the represented organisms.The Web-based motif-x program provides a simple interface to extract statistically significant motifs from large data sets, such as MS/MS post-translational modification data and groups of proteins that share a common biological function. Users upload data files and download results using common Web browsers on essentially any Web-compatible computer. Once submitted, data analyses are performed rapidly on an associated high-speed computer cluster and they produce both syntactic and image-based motif results and statistics. The protocols presented demonstrate the use of motif-x in three common user scenarios.