doi: 10.1093/bioinformatics/10.4.453.
Fast databank searching with a reduced amino-acid alphabet
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- PMID: 7804879
- DOI: 10.1093/bioinformatics/10.4.453
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Fast databank searching with a reduced amino-acid alphabet
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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