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Bioinformatics Vol. 19 no. 4 2003
Pages 506-512
© 2003 Oxford University Press

Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures

Mounir Errami , Christophe Geourjon and Gilbert Deléage *

Pôle de BioInformatique Lyonnais, Institut de Biologie et de Chimie des Protéines, Centre National de la Recherche Scientifique, UMR 5086, 69367 Lyon CEDEX 07, France

Received on March 14, 2002 ; revised on August 26, 2002 ; accepted on October 8, 2002

Motivation: Multiple sequence alignments are essential tools for establishing the homology relations between proteins. Essential amino acids for the function and/or the structure are generally conserved, thus providing key arguments to help in protein characterization. However for distant proteins, it is more difficult to establish, in a reliable way, the homology relations that may exist between them. In this article, we show that secondary structure prediction is a valuable way to validate protein families at low identity rate.

Results: We show that the analysis of the secondary structures compatibility is a reliable way to discard non-related proteins in low identity multiple alignment.

Availability: This validation is possible through our NPS@ server (http://npsa-pbil.ibcp.fr)

Contact: g.deleage{at}ibcp.fr

* To whom correspondence should be addressed.


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