Crystallography and Biocomputing Group

Department of Biochemistry
University of Cambridge

Evolutionary Trace Server (TraceSuite II)

Innis C.A., Shi J. and Blundell T.L. (2000), Protein Eng., 13(12), 839-847.

Server News    Sample Input    Sample Output

Please upload your sequence alignment file here:


Enter your sequence alignment below.

How to Use This Server:

The input alignment should have at least 3 sequences. For better result, use as many sequence homologues as possible. A good coverage over the sequence space of the protein family of interest is essential.

Please use PDB code (e.g. 1abc or 1abcA for chain A) as the name of each known structure in your alignment. We will automatically retrieve PDB coordinates according to the PDB code and its corresponding sequence. If you want to use your own coordinates file that is NOT in PDB, check the section at the bottom of this page.

Acceptable format of the input alignment: PIR (NBRF), CLUSTAL and MSF.

You can also put a HOMSTRAD family code below. Your input sequence alignment (if any) will be aligned to that family and the resulting alignment will be used for the evolutionary trace.

Family code (optional):
Structure + Sequence
Structure only

If you have submitted your sequences to our fold recognition server FUGUE, the family code for each hit is listed in the output, together with the confidence score. (sample)

Number of partitions to trace: (no more than 20)     

Upload your own structure coordinates!
Use this feature ONLY when you want to use structures that are NOT available in the Protein Data Bank (maximum of 3 files allowed).
Make sure your PDB code is consistant with the name shown in your alignment. Recommended (psudeo) PDB code format: 4 letters (e.g. abcd)
Make sure your PDB file is consistant with the corresponding sequence in your alignment (i.e. No extra residues in the PDB file or in the sequence).

PDB code 1: ----> PDB file 1:
PDB code 2: ----> PDB file 2:
PDB code 3: ----> PDB file 3:

Suggestions and comments to Jiye Shi (gudeng7 AT