FAST DATA-BANK SEARCHING WITH A REDUCED AMINO-ACID ALPHABET

Authors
LANDES C RISLER JL
Citation
C. Landes et Jl. Risler, FAST DATA-BANK SEARCHING WITH A REDUCED AMINO-ACID ALPHABET, Computer applications in the biosciences, 10(4), 1994, pp. 453-454
Citations number
12
Categorie Soggetti
Mathematical Methods, Biology & Medicine","Computer Sciences, Special Topics","Computer Science Interdisciplinary Applications","Biology Miscellaneous
Journal title
Computer applications in the biosciences → ACNP
ISSN journal
02667061
Volume
10
Issue
4
Year of publication
1994
Pages
453 - 454
Database
ISI
SICI code
0266-7061(1994)10:4<453:FDSWAR>2.0.ZU;2-I
Abstract
Fast sequence databanks search algorithms generally make use of hash t ables 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 a lphabet reduced to 10 symbols, that we used in modified versions of th e FASTP and SCAN programs. An application to the aminoacyl-tRNA synthe tases shows that this technique may be useful in detecting distant rel ationships between proteins.