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.
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