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Nucleic Acids Research, 2003, Vol. 31, No. 13 3789-3791
© 2003 Oxford University Press

UniqueProt: creating representative protein sequence sets

Sven Mika*,1,2 and Burkhard Rost1,3,4

1 CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA 2 Institute of Physical Biochemistry, University Witten/Herdecke, Stockumer Strasse 10, 58448 Witten, Germany 3 Columbia University Center for Computational Biology and Bioinformatics (C2B2), Russ Berrie Pavilion, 1150 St Nicholas Avenue, New York, NY 10032, USA 4 North East Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street BB217, New York, NY 10032, USA

*To whom correspondence should be addressed. Tel: +1 2123054018, Fax: +1 2123057932; Email: mika{at}cubic.bioc.columbia.edu

UniqueProt is a practical and easy to use web service designed to create representative, unbiased data sets of protein sequences. The largest possible representative sets are found through a simple greedy algorithm using the HSSP-value to establish sequence similarity. UniqueProt is not a real clustering program in the sense that the ‘representatives’ are not at the centres of well-defined clusters since the definition of such clusters is problem-specific. Overall, UniqueProt is a reasonable fast solution for bias in data sets. The service is accessible at http://cubic.bioc.columbia.edu/services/uniqueprot; a command-line version for Linux is downloadable from this web site.


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