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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 validatedoi:10.1093/bioinformatics/btg016 pmid:12611806 fatcat:hd7fohpvwbb45j7mqcwgxz5nua