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© Oxford University Press

Fast databank searching with a reduced amino-acid alphabet

Claudine Landès 1 and Jean-Loup Risler

Centre de Génétique Moléculaire du CNRS 91198 Gif sur Yvette Cedex France

1To whom reprint requests should be sent

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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