REP2：一个用于检测蛋白质序列中常见串联重复的网络服务器。

REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences.

机构信息

Department of Computer Science, Faculty of Mathematics and Informatics, University of M'sila, 28000 M'sila, Algeria; Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany.

Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany.

出版信息

J Mol Biol. 2021 May 28;433(11):166895. doi: 10.1016/j.jmb.2021.166895. Epub 2021 Feb 24.

DOI:10.1016/j.jmb.2021.166895

PMID:33972020

Abstract

Ensembles of tandem repeats (TRs) in protein sequences expand rapidly to form domains well suited for interactions with proteins. For this reason, they are relatively frequent. Some TRs have known structures and therefore it is advantageous to predict their presence in a protein sequence. However, since most TRs diverge quickly, their detection by classical sequence comparison algorithms is not very accurate. Previously, we developed a method and a web server that used curated profiles and thresholds for the detection of 11 common TRs. Here we present a new web server (REP2) that allows the analysis of TRs in both individual and aligned sequences. We provide currently precomputed analyses for a selection of 78 UniProt reference proteomes. We illustrate how these data can be used to study the evolution of TRs using comparative genomics. REP2 can be accessed at http://cbdm-01.zdv.uni-mainz.de/~munoz/rep/.

摘要

蛋白质序列中的串联重复（TR）集合会迅速扩展，从而形成与蛋白质相互作用的良好结构域。由于这个原因，它们相对频繁。一些 TR 具有已知的结构，因此预测它们在蛋白质序列中的存在是有利的。然而，由于大多数 TR 迅速分化，因此经典序列比较算法对它们的检测不太准确。之前，我们开发了一种方法和一个网络服务器，该方法和网络服务器使用精心策划的配置文件和阈值来检测 11 种常见的 TR。在这里，我们提供了一个新的网络服务器（REP2），它允许分析单个和对齐序列中的 TR。我们目前为 78 个 UniProt 参考蛋白质组提供了预先计算的分析。我们说明了如何使用比较基因组学来研究 TR 的进化。REP2 可在 http://cbdm-01.zdv.uni-mainz.de/~munoz/rep/ 访问。