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This article is part of the supplement: Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009)

Open Access Research

Improved algorithms for approximate string matching (extended abstract)

Dimitris Papamichail1* and Georgios Papamichail2

Author Affiliations

1 Department of Computer Science, University of Miami, Coral Gables, Miami, USA

2 National Center of Public Administration, Athens, Greece

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BMC Bioinformatics 2009, 10(Suppl 1):S10  doi:10.1186/1471-2105-10-S1-S10

Published: 30 January 2009

Abstract

Background

The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants of the problem, including comparison of two strings, approximate pattern identification in a string or calculation of the longest common subsequence that two strings share.

Results

We designed an output sensitive algorithm solving the edit distance problem between two strings of lengths n and m respectively in time O((s - |n - m|)·min(m, n, s) + m + n) and linear space, where s is the edit distance between the two strings. This worst-case time bound sets the quadratic factor of the algorithm independent of the longest string length and improves existing theoretical bounds for this problem. The implementation of our algorithm also excels in practice, especially in cases where the two strings compared differ significantly in length.

Conclusion

We have provided the design, analysis and implementation of a new algorithm for calculating the edit distance of two strings with both theoretical and practical implications. Source code of our algorithm is available online.