University of Leipzig, Institute of Medical Physics and Biophysics, Härtelstr. 16-18, 04107 Leipzig, Germany.
Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
Nucleic Acids Res. 2022 Jul 5;50(W1):W29-W35. doi: 10.1093/nar/gkac391.
The AlignMe web server is dedicated to accurately aligning sequences of membrane proteins, a particularly challenging task due to the strong evolutionary divergence and the low compositional complexity of hydrophobic membrane-spanning proteins. AlignMe can create pairwise alignments of either two primary amino acid sequences or two hydropathy profiles. The web server for AlignMe has been continuously available for >10 years, supporting 1000s of users per year. Recent improvements include anchoring, multiple submissions, and structure visualization. Anchoring is the ability to constrain a position in an alignment, which allows expert information about related residues in proteins to be incorporated into an alignment without manual modification. The original web interface to the server limited the user to one alignment per submission, hindering larger scale studies. Now, batches of alignments can be initiated with a single submission. Finally, to provide structural context for the relationship between proteins, sequence similarity can now be mapped onto one or more structures (or structural models) of the proteins being aligned, by links to MutationExplorer, a web-based visualization tool. Together with a refreshed user interface, these features further enhance an important resource in the membrane protein community. The AlignMe web server is freely available at https://www.bioinfo.mpg.de/AlignMe/.
AlignMe 网页服务器致力于精确地对齐膜蛋白序列，这是一项极具挑战性的任务，因为疏水性跨膜蛋白具有强烈的进化分歧和低组成复杂性。AlignMe 可以创建两个原始氨基酸序列或两个疏水性图谱的两两比对。AlignMe 的网页服务器已经连续运行了 10 多年，每年支持数千名用户。最近的改进包括锚定、多次提交和结构可视化。锚定是约束对齐中某个位置的能力，它允许将有关蛋白质中相关残基的专家信息纳入对齐，而无需手动修改。该服务器的原始网页界面限制用户每次提交一个对齐，阻碍了更大规模的研究。现在，只需一次提交即可启动多个对齐批次。最后，为了提供蛋白质之间关系的结构背景，现在可以通过链接到基于网络的可视化工具 MutationExplorer，将序列相似性映射到正在对齐的蛋白质的一个或多个结构（或结构模型）上。这些功能与更新后的用户界面一起，进一步增强了膜蛋白社区中的一个重要资源。AlignMe 网页服务器可免费在 https://www.bioinfo.mpg.de/AlignMe/ 获取。
