Subset Seed Automaton
- Cite this paper as:
- Kucherov G., Noé L., Roytberg M. (2007) Subset Seed Automaton. In: Holub J., Žďárek J. (eds) Implementation and Application of Automata. CIAA 2007. Lecture Notes in Computer Science, vol 4783. Springer, Berlin, Heidelberg
We study the pattern matching automaton introduced in  for the purpose of seed-based similarity search. We show that our definition provides a compact automaton, much smaller than the one obtained by applying the Aho-Corasick construction. We study properties of this automaton and present an efficient implementation of the automaton construction. We also present some experimental results and show that this automaton can be successfully applied to more general situations.
Keywordsspaced seed subset seed automaton seed sensitivity
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