Run AlignMe in pair-wise mode

1. Provide sequences
This form allows you to align protein sequences. Each input sequence has 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.



In standard submissions, the user is expected to provide a single fasta sequence in each of the two boxes below. The output will be a single pairwise alignment.
However, a batch mode is available to enable the user to easily calculate many pairwise alignments in a single submission. Thus, if more than one sequence is provided in a given box, then all those sequences will be aligned (pairwise) with the sequences in the other box. The results will be reported as a set of pairwise alignments. Every input sequence should be in fasta format as above. Please note that this is not the same as a multiple-sequence alignment.

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. Anchors
Anchors allow for aligning certain positions or motifs that might not be aligned running an unbiased alignment.
Each anchor consists of the residue identifier in the first sequence, the residue ID in the second sequence and a weight, specifying the strengths of the anchor.
The first amino acid has the residue ID '1'.
A high weight will enforce the anchor.
The default in the form is set to 1000, which will enforce this anchor.
Either enter them using the form above or as a file with the following format:
	12	24	10.0
	123     78       5.0

For batch submissions (i.e. multiple pairwise alignments) anchors can also be specified, by uploading a file and indiciating the sequence number next to the anchor position. For example:
        1:7     5:7     1000
will fix position 7 in sequences 1 and 5 in the corresponding alignment and assumes that at least 5 sequences have been provided in the second box.

Comment lines need to be removed!

Residue 1 Residue 2 Weight
Add more anchors
...or upload an anchor file?

4. 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.

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