A New Algorithm for Fast All-Against-All Substring Matching
We present a new and efficient algorithm to solve the ’threshold all vs. all’ problem, which involves searching of two strings (with length N and M respectively) for finding all maximal approximate matches of length at least S and with up to K differences. The algorithm is based on a novel graph model, and it solves the problem in time O(NMK 2).
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- 1.Baeza-Yates, R.A., Gonnet, G.H.: All-against-all sequence matching. Rep. Dept. of CS, U. de Chile (1990)Google Scholar
- 2.Baeza-Yates, R.A., Gonnet, G.H.: A fast algorithm on average for all-against-all sequence matching. In: Proc. SPIRE/CRIWG 1999, pp. 16–23 (1999)Google Scholar
- 3.Barsky, M., Stege, U., Thomo, A., Upton, C.A.: A New Algorithm for Fast All-Against-All Substring Matching (2006), http://www.cs.uvic.ca/~mgbarksy/apbt.pdf
- 5.Pevzner, P., Sze, S.H.: Combinatorial approaches to finding subtle signals in DNA sequences. In: Proc. ISMB 2000, pp. 269–278 (2000)Google Scholar
- 8.Vilo, J.: Pattern Discovery from Biosequences. PhD Thesis, Series of Publications A, Report A-2002-3 U. of Helsinki, Finland (2002)Google Scholar
- 9.Virus Orthologous Clusters database at Viral Bioinformatics Resource Center, U. of Victoria, Canada, http://athena.bioc.uvic.ca