Welcome to the AlignMe manual

Please follow the links to learn more about how to use AlignMe:

• Introduction to AlignMe
• Running AlignMe on the web server
• Installing AlignMe
• Running AlignMe on your local machine
• Release Notes

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Web Server

The webserver for running the AlignMe code, including transmembrane and secondary structure predictions, is available at: http://www.bioinfo.mpg.de/AlignMe

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Citing AlignMe

If you use AlignMe for your research and study, please cite the following references:

For anchors:

Staritzbichler, R, Sarti E, Yaklich, E, Aleksandrova, AA, Stamm, M, Khafizov, K, and LR Forrest 2021 PloS One 16(4): e0239881

For pairwise alignments:

Stamm, M, Staritzbichler, R, Khafizov, K, and LR Forrest. 2013 “Alignment of Helical Membrane Protein Sequences Using AlignMe” PloS One 8(3):e57731

For the server or alignments using “Fast mode”:

Stamm, M, Staritzbichler, R, Khafizov, K, and LR Forrest. 2014 “AlignMe--a Membrane Protein Sequence Alignment Web Server” Nucleic Acids Research 42 (Web Server issue): W246-51

For the alignment of two multiple-sequence alignments:

Khafizov, K, Staritzbichler, R, Stamm, M and LR Forrest. 2010 “A Study of the Evolution of Inverted-Topology Repeats from LeuT-Fold Transporters Using AlignMe” Biochemistry 49(50): 10702-10713