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.
Pham
Tuan D
TD
School of Computing and Information Technology, Griffith University, Nathan Campus, QLD 4111, Australia. t.pham@griffith.edu.au <t.pham@griffith.edu.au>
Zuegg
Johannes
J
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