A probabilistic measure for alignment-free sequence comparison.
BACKGROUND
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.


RESULTS
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).


BACKGROUND
All datasets and computer codes written in MATLAB are available upon request from the first author.
School of Computing and Information Technology, Griffith University, Nathan Campus, QLD 4111, Australia. t.pham@griffith.edu.au <t.pham@griffith.edu.au>
Tuan D
TD
Pham
Johannes
J
Zuegg
D000465:Algorithms; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics; D008957:Models, Genetic; D015233:Models, Statistical; D009876:Operon / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012763:Shigella flexneri / Q000235:genetics; D013912:Threonine / Q000235:genetics
D013912:Threonine