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String Matching in the DNA Alphabet
Author(s) -
TARHIO JORMA,
PELTOLA HANNU
Publication year - 1997
Publication title -
software: practice and experience
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.437
H-Index - 70
eISSN - 1097-024X
pISSN - 0038-0644
DOI - 10.1002/(sici)1097-024x(199707)27:7<851::aid-spe108>3.0.co;2-d
Subject(s) - alphabet , transformation (genetics) , string searching algorithm , computer science , string (physics) , algorithm , matching (statistics) , pattern matching , theoretical computer science , mathematics , artificial intelligence , biology , genetics , philosophy , linguistics , statistics , mathematical physics , gene
Searching for long DNA strings is studied. A q ‐gram variation of the Boyer–Moore algorithm is considered. An alphabet transformation with precomputed tables is utilized to reduce the processing time. Experimental results show that the new algorithm is efficient in practice. © 1997 John Wiley & Sons, Ltd.