Approximate string searching with fast fourier transforms and simplexes
Torrey Pines High School, San Diego, California, United States
- Published
- Accepted
- Subject Areas
- Algorithms and Analysis of Algorithms
- Keywords
- fast fourier transform, Hamming distance, string searching, don't cares, simplex
- Copyright
- © 2019 Liu
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. Approximate string searching with fast fourier transforms and simplexes. PeerJ Preprints 7:e27615v1 https://doi.org/10.7287/peerj.preprints.27615v1
Abstract
Previous algorithms for solving the approximate string matching with Hamming distance problem with wildcard ("don't care") characters have been shown to take \(O(|\Sigma| N \log M)\) time, where \(N\) is the length of the text, \(M\) is the length of the pattern, and \(|\Sigma|\) is the size of the alphabet. They make use of the Fast Fourier Transform for efficiently calculating convolutions. We describe a novel approach of the problem, which makes use of special encoding schemes that depend on \((|\Sigma| - 1)\)-simplexes in \((|\Sigma| - 1)\)-dimensional space.
Author Comment
This is a preprint submission to PeerJ Preprints.