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Sequence Harmony


Sequence Harmony is an entropy-based method, which accurately detects subfamily specific functional sites from a multiple sequence alignment. The algorithm implements a new formula, able to score compositional differences between subfamilies in a simple manner on an intuitive scale.

Information on the Input format

More on Method Background

If you use our method, please cite:
Feenstra KA, Pirovano WA, Krab K and Heringa J. Sequence Harmony: Detecting Functional Specificity from Alignments. Nucl. Acids Res., 2007, Vol. 35, W495-W498.
Pirovano WA1, Feenstra KA1 and Heringa J. Sequence Comparison by Sequence Harmony Identifies Subtype Specific Functional Sites. Nucl. Acids Res., 2006, Vol. 34, No. 22 6540-6548.
1 joint first authors


Paste in a multiple alignment in fasta format:

Or Upload a multiple alignment in fasta format:

(you can use the small example for a test-ride)

Give the identifier of the first sequence of the second subgroup:


Advanced Features

Sequence Harmony cutoff value: (values between 0-1 make sense)

Reference Sequence (optional):

Reference Structure (optional):
PDB identifier OR PDB file All chains in the PDB file will be aligned against your input alignment and the best match(es) chosen.
To manually align the PDB file with your input alignment, specify the starting position to match the numbering of your reference sequence to that of the PDB file. Starting position can be positive or negative.



The Sequence Harmony web server developed and Copyright (c) by K. Anton Feenstra and Walter Pirovano

(c) IBIVU 2021. If you are experiencing problems with the site, please contact the webmaster.