Fast Searching for Multiple Keywords in Multiple Texts

Aho-Corasick is an optimal algorithm for finding many keywords in a text. It can locate all matches in a text in O(N+M) time; i.e., the time needed scales linearly with the number of keywords (N) and the size of the text (M). Compare this to the naive approach which takes O(N*M) time to loop through each pattern and scan for it in the text. This implementation builds the trie (the generic name of the data structure) and runs the search in a single function call. If you want to search multiple texts with the same trie, the function will take a list or vector of texts and return a list of matches to each text. By default, all 128 ASCII characters are allowed in both the keywords and the text. A more efficient trie is possible if the alphabet size can be reduced. For example, DNA sequences use at most 19 distinct characters and usually only 4; protein sequences use at most 26 distinct characters and usually only 20. UTF-8 (Unicode) matching is not currently supported.


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0.1.2 by Matt Chambers, 7 months ago

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Authors: Matt Chambers [aut, cre] , Tomas Petricek [aut, cph] , Vanderbilt University [cph]

Documentation:   PDF Manual  

Apache License 2.0 license

Imports Rcpp

Suggests Biostrings, microbenchmark, testthat

Linking to Rcpp

System requirements: C++11

Imported by prozor.

See at CRAN