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Updated: Aug 1, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
Fast databank searching with a reduced amino-acid alphabet
1Centre de Génétique Moléculaire du CNRS, Gif sur Yvette, France.
Abstract:
Fast sequence databanks search algorithms generally make use of hash tables and look for exactly matching words. An increased sensitivity--at the expense of a decreased selectivity--can be attained in the case of proteins by using a reduced amino acid alphabet. We propose here an alphabet reduced to 10 symbols, that we used in modified versions of the FASTP and SCAN programs. An application to the aminoacyl-tRNA synthetases shows that this technique may be useful in detecting distant relationships between proteins.
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