Skip Navigation

This Article
Right arrow Full Text (Print PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Nicola, P.
Right arrow Articles by Pasole, G.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Nicola, P.
Right arrow Articles by Pasole, G.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© Oxford University Press

FASTPAT: a fast and efficient algorithm for string searching in DNA sequences

Prunella Nicola , Sabino Liuni 1, Marcella Attimonelli 2 and Graziano Pasole 2

Digital Equipment S.p.A. Bari, Italy
1CSMME-CNR Bari, Italy
2Dipartimento di Biochimica e Biologia Molecolare Bari, Italy

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.

Received on November 10, 1992; accepted on February 25, 1993

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.