FASTPAT: a fast and efficient algorithm for string searching in DNA sequences.
A new string searching algorithm is presented aimed at searching for the occurrence of character patterns in longer character texts. The algorithm, specifically designed for nucleic acid sequence data, is essentially derived from the Boyer-Moore method (Comm. ACM, 20, 762-772, 1977). Both pattern and text data are compressed so that the natural 4-letter alphabet of nucleic acid sequences is considerably enlarged. The string search starts from the last character of the pattern and proceeds in large jumps through the text to be searched. The data compression and searching algorithm allows one to avoid searching for patterns not present in the text as well as to inspect, for each pattern, all text characters until the exact match with the text is found. These considerations are supported by empirical evidence and comparisons with other methods.
Prunella
N
N
Digital Equipment S.p.A., Bari, Italy.
Liuni
S
S
Attimonelli
M
M
Pesole
G
G
D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000235:genetics; D016208:Databases, Factual; D008969:Molecular Sequence Data; D010363:Pattern Recognition, Automated; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000706:statistics & numerical data; D012984:Software
D004247:DNA