Pclust：蛋白质网络可视化，突出显示实验数据。
Pclust: protein network visualization highlighting experimental data.
机构信息
Departments of Biophysics and Biochemistry and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA.
出版信息
Bioinformatics. 2013 Oct 15;29(20):2647-8. doi: 10.1093/bioinformatics/btt451. Epub 2013 Aug 5.
SUMMARY
One approach to infer functions of new proteins from their homologs utilizes visualization of an all-against-all pairwise similarity network (A2ApsN) that exploits the speed of BLAST and avoids the complexity of multiple sequence alignment. However, identifying functions of the protein clusters in A2ApsN is never trivial, due to a lack of linking characterized proteins to their relevant information in current software packages. Given the database errors introduced by automatic annotation transfer, functional deduction should be made from proteins with experimental studies, i.e. 'reference proteins'. Here, we present a web server, termed Pclust, which provides a user-friendly interface to visualize the A2ApsN, placing emphasis on such 'reference proteins' and providing access to their full information in source databases, e.g. articles in PubMed. The identification of 'reference proteins' and the ease of cross-database linkage will facilitate understanding the functions of protein clusters in the network, thus promoting interpretation of proteins of interest.
AVAILABILITY
The Pclust server is freely available at http://prodata.swmed.edu/pclust
摘要
从同源蛋白推断新蛋白功能的一种方法是利用全对全两两相似性网络（A2ApsN）的可视化，该方法利用了 BLAST 的速度，避免了多重序列比对的复杂性。然而，由于当前软件包中缺乏将具有特征的蛋白质与其相关信息联系起来的方法，因此识别 A2ApsN 中的蛋白质簇的功能绝非易事。由于自动注释转移引入的数据库错误，应该从具有实验研究的蛋白质（即“参考蛋白质”）中进行功能推导。在这里，我们提出了一个名为 Pclust 的网络服务器，它提供了一个用户友好的界面来可视化 A2ApsN，重点关注这些“参考蛋白质”，并提供对其在源数据库中的完整信息的访问，例如 PubMed 中的文章。“参考蛋白质”的识别和跨数据库链接的容易性将有助于理解网络中蛋白质簇的功能，从而促进对感兴趣的蛋白质的解释。
可用性
Pclust 服务器可免费在 http://prodata.swmed.edu/pclust 获得。
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