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Bioinformatics. 2004 Dec 12;20(18):3455-61. Epub 2004 Jul 22.

A probabilistic measure for alignment-free sequence comparison.

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School of Computing and Information Technology, Griffith University, Nathan Campus, QLD 4111, Australia. <>



Alignment-free sequence comparison methods are still in the early stages of development compared to those of alignment-based sequence analysis. In this paper, we introduce a probabilistic measure of similarity between two biological sequences without alignment. The method is based on the concept of comparing the similarity/dissimilarity between two constructed Markov models.


The method was tested against six DNA sequences, which are the thrA, thrB and thrC genes of the threonine operons from Escherichia coli K-12 and from Shigella flexneri; and one random sequence having the same base composition as thrA from E.coli. These results were compared with those obtained from CLUSTAL W algorithm (alignment-based) and the chaos game representation (alignment-free). The method was further tested against a more complex set of 40 DNA sequences and compared with other existing sequence similarity measures (alignment-free).


All datasets and computer codes written in MATLAB are available upon request from the first author.

[Indexed for MEDLINE]

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