The Barton Group


Analyse Multiple Aligned Sequences

This server allows you to run AMAS on your own multiple sequence alignment. If you would like to run AMAS on your own computer, you can obtain the package by following the instructions on our WWW pages. You can also read the paper that describes the AMAS algorithm.

You may find the AMAS manual helpful. This describes the program and file formats.

You can try the example alignment file (in AMPS format) and corresponding "Sensible Groups" file. Click the button below to insert the example files into the input boxes.

Select the format of your input alignment:

Paste the alignment here:
or upload an alignment file:

Sensible Groups. These define which sets of sequences in the alignment will be compared by AMAS. Each group is shown on a separate line either as a range of sequence numbers, or a set of discrete sequence numbers. These need not include all the sequences in your alignment. For example, if you have an alignment of 20 sequences, you might want to define sequences 1-5 as one group, 6 and 8 as a second, and 15-20 as a third. This would be shown as:
Enter "Sensible Groups" here:

Select property table:
extra_ul is for extracellular proteins, intra_ul is for intracellular. This just affects the treatment of Cys. extra is a good default. There are other property tables supplied with AMAS and you can devise your own, but these features aren't available on this server.

Select the conservation threshold:

This is the most useful parameter to fiddle with. Higher numbers highlight more highly conserved positions, lower numbers highlight less conserved positions. Values between 5 and 10 are worth trying with the property tables available here; 7 is a good default starting point.

You can set some of the many AMAS options here. See the AMAS manual for details.

Font size for PostScript output
Output orientation
Ignore atypical residues (percentage)
Number of gaps to ignore per sub group
Frequency histogram, or similarity/difference report
  If histogram, enter height for bars
Show identifiers or numbers in report file
Mask amino acids at unconserved positions No. Yes.
Only produce the highlighted alignment No. Yes.

The results of your analysis will persist for 30 MINUTES before being deleted.