AlignMe (for 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.

Help can be found in any section of the forms by clicking on the red buttons. Examples can be processed by clicking on the Example-Button on top of each section. Additionally there is a FAQ!

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

Download AlignMe 1.1

  source code download of AlignMe 1.1 incl. examples

  manual for the standalone version of AlignMe 1.1

A changelog and older versions are available at


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AlignMe was written in C++ in the Forrest lab by:
Rene Staritzbichler, Marcus Stamm and Kamil Khafizov

Khafizov K, Staritzbichler R, Stamm M and LR Forrest (2014) Nucl. Acids Res. 42(W1), W246-251
Stamm M, Staritzbichler R, Khafizov K and LR Forrest (2013) PLoS ONE 8(3), e57731. doi:10.1371/journal.pone.0057731
Khafizov K, Staritzbichler R, Stamm M and LR Forrest (2011) Biochemistry 49(50), 10702-10713