1. Fast databank searching with a reduced amino-acid alphabet.
- Author
-
Landès C and Risler JL
- Subjects
- Algorithms, Amino Acid Sequence, Amino Acyl-tRNA Synthetases genetics, Escherichia coli enzymology, Escherichia coli genetics, Molecular Sequence Data, Oligopeptides genetics, Sequence Alignment methods, Terminology as Topic, Databases, Factual, Proteins genetics, Software
- 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.
- Published
- 1994
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