AlignMe

Run AlignMe in pair-wise mode


1. Provide sequences
This form allows you to align protein sequences. Both sequences have to be in fasta format, which consists of a header starting with ">" followed by a name or description of the sequence, and the sequence in the following lines.


Example:

>1KPL.pdb CHAIN_ID: A
TPLAILFMAAVVGTLTGLVGVAFEKAVSWVQNMRIGALVQVADHAFLL
WPLAFILSALLAMVGYFLVRKFAPEAGGSGIPEIEGALEELRPVRWWR
VLPVKFIGGMGTLGAGMVLGREGPTV

Enter a sequence in fasta format: Enter another sequence in fasta format:

...or upload a fasta file:

...or upload another fasta file:


2. Select optimized or user-defined parameters
Gap penalties and the choice of input parameters have been optimized for transmembrane proteins based on the HOMEP 2010 data set. We recommend that you use these parameters only for aligning transmembrane proteins and only if you know the secondary structure of the proteins.

Parameters for α-helical membrane proteins

AlignMe PST
Most accurate alignments for very distantly related proteins, <15% identity;
~9 mins for a 179 and 215-residue sequence pair
AlignMe PS
Most accurate alignments for low-homology proteins, ~15-45% identity;
~5 mins for a 179 and 215-residue sequence pair
AlignMe P
Most accurate alignments for very closely related proteins, >45% identity;
~5 mins for a 179 and 215-residue sequence pair
Fast, but less accurate alignments (~3 seconds)
based on a substitution matrix and a hydrophobicity scale
slower, but more accurate ~10 min
(substitution matrix, hydrophobicity scale
& secondary structure prediction)

Parameters for β-barrel membrane proteins

Fast (~3 seconds)
based on substitution matrix & hydrophobicity scale

Or use your own alignment parameters

Define your own parameters

         Show detailed alignment parameter options


3. Submit

Enter an e-mail address to receive a message containing your results.
This is recommended for "Most accurate alignments" and alignments with
automated PSSM calculations, PSIPRED or OCTOPUS predictions.

MPG | MPI BP | NIH | NINDS
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