Fast databank searching with a reduced amino-acid alphabet.
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.
Landès
C
C
Centre de Génétique Moléculaire du CNRS, Gif sur Yvette, France.
Risler
J L
JL
D000465:Algorithms; D000595:Amino Acid Sequence; D000604:Amino Acyl-tRNA Synthetases / Q000235:genetics; D016208:Databases, Factual; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000235:genetics; D011506:Proteins / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D012984:Software; D009626:Terminology as Topic
D009842:Oligopeptides; D011506:Proteins; D000604:Amino Acyl-tRNA Synthetases