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. 1994 Jul;10(4):453-4.
doi: 10.1093/bioinformatics/10.4.453.

Fast databank searching with a reduced amino-acid alphabet

C Landès  1 , J L Risler
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Fast databank searching with a reduced amino-acid alphabet

C Landès et al. Comput Appl Biosci. 1994 Jul.

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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