Welcome to the AlignMe Web Server

AlignMe (for sequence Alignment of Membrane Proteins) is a very flexible sequence alignment program that allows the use of various different measures of similarity. These similarity measures include: substitution matrices, hydrophobicity scales and any kind of profiles (i.e. secondary structure predictions or transmembrane predictions). AlignMe can be used to examine detailed similarity between homologous proteins even if there is no notable sequence similarity. The predefined gap/weight sets have been optimized for membrane proteins, and so should be particularly useful for these difficult cases. This webserver is currently running version 1.2.

Help can be found in any section of the forms by clicking on the "i" buttons. Examples can be processed by clicking on the "Generate example input" Button at the top of each section. Additionally there is an FAQ page.

Modes of use

AlignMe pairwise pairwise (PW) alignment of two sequences, using any combination of scales and profiles
AlignMe profile-profile profile-profile (PP) alignment of two multiple sequence alignments


  source code of AlignMe 1.1 incl. examples

  source code of AlignMe 1.2 incl. examples

  manual for the standalone version of AlignMe 1.1

See also:

Credits & Citations

AlignMe was written by René Staritzbichler, Marcus Stamm, and Kamil Khafizov in the Forrest lab, formerly at the Max Planck Institute of Biophysics. The webservice is hosted at the Max Planck Gesellschaft, with thanks to Markus Rampp and the HPC application support team. Ongoing development and support is provided by Edoardo Sarti, René Staritzbichler, and Lucy Forrest and by NINDS.

If you use AlignMe, please cite:
Khafizov K, Staritzbichler R, Stamm M and LR Forrest (2014) Nucl. Acids Res. 42:W246-251
Stamm M, Staritzbichler R, Khafizov K and LR Forrest (2013) PLoS ONE 8:e57731
Khafizov K, Staritzbichler R, Stamm M and LR Forrest (2011) Biochemistry 49:10702-10713

Feedback and contact:

NINDS Copyright 2017