Department of Computer Networks and Systems, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland.
Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland.
Nucleic Acids Res. 2020 Jul 2;48(W1):W77-W84. doi: 10.1093/nar/gkaa339.
Low complexity regions (LCRs) in protein sequences are characterized by a less diverse amino acid composition compared to typically observed sequence diversity. Recent studies have shown that LCRs may co-occur with intrinsically disordered regions, are highly conserved in many organisms, and often play important roles in protein functions and in diseases. In previous decades, several methods have been developed to identify regions with LCRs or amino acid bias, but most of them as stand-alone applications and currently there is no web-based tool which allows users to explore LCRs in protein sequences with additional functional annotations. We aim to fill this gap by providing PlaToLoCo - PLAtform of TOols for LOw COmplexity-a meta-server that integrates and collects the output of five different state-of-the-art tools for discovering LCRs and provides functional annotations such as domain detection, transmembrane segment prediction, and calculation of amino acid frequencies. In addition, the union or intersection of the results of the search on a query sequence can be obtained. By developing the PlaToLoCo meta-server, we provide the community with a fast and easily accessible tool for the analysis of LCRs with additional information included to aid the interpretation of the results. The PlaToLoCo platform is available at: http://platoloco.aei.polsl.pl/.
蛋白质序列中的低复杂度区域（LCR）的氨基酸组成与通常观察到的序列多样性相比，具有较低的多样性。最近的研究表明，LCR 可能与固有无序区域共同出现，在许多生物体中高度保守，并且经常在蛋白质功能和疾病中发挥重要作用。在过去的几十年中，已经开发了几种方法来识别具有 LCR 或氨基酸偏倚的区域，但大多数方法都是独立的应用程序，目前没有基于网络的工具可以允许用户使用其他功能注释来探索蛋白质序列中的 LCR。我们旨在通过提供 PlaToLoCo - LOw COmplexity 的工具平台来填补这一空白，这是一个元服务器，它集成并收集了五个用于发现 LCR 的最先进工具的输出，并提供了功能注释，如域检测、跨膜片段预测和氨基酸频率计算。此外，还可以获得查询序列上搜索结果的并集或交集。通过开发 PlaToLoCo 元服务器，我们为社区提供了一个快速且易于访问的工具，用于分析具有附加信息的 LCR，以帮助解释结果。PlaToLoCo 平台可在：http://platoloco.aei.polsl.pl/ 获得。
