PR2ALIGN: protein sequence alignment using weighted profiles of biochemical properties


This web-server finds an optimal minimal distance global alignment of two amino acid sequences based on the comparison of the profiles of biochemical properties of these sequences. Unlike traditional amino acid sequence alignment methods that use a fixed 20x20 matrix to score matches and mismatches, PR2ALIGN measures the distance between pairs of aligned residues using a set of weighted biochemical properties of amino acids. The user can provide any number of amino acid properties (such as hydrophobicity, size, charge, etc) and specify a weight for each property. The higher the weight for a given property, the more this property affects the final alignment. For more details please refer to the help link.

Amino acid properties to use for the alignment


Retrieval of the results

E-mail the results. E-mail address:
Display a URL link to my process.
(Data are kept on the web server for 3 days, and deleted afterwards)


I.B.Kuznetsov and M.McDuffie, 2015, PR2ALIGN: a stand-alone software program and a web-server for protein sequence alignment
using weighted biochemical properties of amino acids. BMC Research Notes, 8:187

Click here to download the source code
Please address your questions and comments to Igor Kuznetsov
Web-design: Michael McDuffie
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