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

Abstract

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. We show that the analysis of the secondary structures compatibility is a reliable way to discard non-related proteins in low identity multiple alignment. This validation is possible through our NPS@ server (http://npsa-pbil.ibcp.fr)