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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\u00a0&amp;gt;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,\u00a0batches of alignments\u00a0can be initiated\u00a0with 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\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac391","type":"journal-article","created":{"date-parts":[[2022,5,11]],"date-time":"2022-05-11T13:43:23Z","timestamp":1652276603000},"page":"W29-W35","source":"Crossref","is-referenced-by-count":5,"title":["AlignMe: an update of the web server for alignment of membrane protein sequences"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6719-2997","authenticated-orcid":false,"given":"Ren\u00e9","family":"Staritzbichler","sequence":"first","affiliation":[{"name":"University of Leipzig, Institute of Medical Physics and Biophysics , H\u00e4rtelstr. 16-18, 04107 Leipzig , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6548-1840","authenticated-orcid":false,"given":"Emily","family":"Yaklich","sequence":"additional","affiliation":[{"name":"Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD 20892 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2417-1448","authenticated-orcid":false,"given":"Edoardo","family":"Sarti","sequence":"additional","affiliation":[{"name":"Algorithms, Biology, Structure Unit Inria Sophia Antipolis \u2013 M\u00e9diterran\u00e9e , 06902 Valbonne, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikola","family":"Ristic","sequence":"additional","affiliation":[{"name":"University of Leipzig, Institute of Medical Physics and Biophysics , H\u00e4rtelstr. 16-18, 04107 Leipzig , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0063-1104","authenticated-orcid":false,"given":"Peter\u00a0W","family":"Hildebrand","sequence":"additional","affiliation":[{"name":"University of Leipzig, Institute of Medical Physics and Biophysics , H\u00e4rtelstr. 16-18, 04107 Leipzig , Germany"},{"name":"Charit\u00e9 \u2013Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Institute of Medical Physics and Biophysics , 10117 Berlin , Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1855-7985","authenticated-orcid":false,"given":"Lucy\u00a0R","family":"Forrest","sequence":"additional","affiliation":[{"name":"Computational Structural Biology Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health , Bethesda , MD 20892 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,24]]},"reference":[{"key":"2022070500021058300_B1","doi-asserted-by":"crossref","first-page":"2874","DOI":"10.1093\/molbev\/msw164","article-title":"Membrane proteins are dramatically less conserved than water-soluble proteins across the tree of life","volume":"33","author":"Sojo","year":"2016","journal-title":"Mol. 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