A probabilistic measure for alignment-free sequence comparison. Export

@article{citeulike:552902, abstract = {MOTIVATION: 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). AVAILABILITY: All datasets and computer codes written in MATLAB are available upon request from the first author.}, address = {School of Computing and Information Technology, Griffith University, Nathan Campus, QLD 4111, Australia. t.pham@griffith.edu.au <t.pham@griffith.edu.au>}, author = {Pham, T. D. and Zuegg, J.}, citeulike-article-id = {552902}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/15271780}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=15271780}, day = {12}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {alignment-free, comparison, sequence}, month = {December}, number = {18}, pages = {3455--3461}, posted-at = {2008-11-22 21:26:36}, priority = {2}, title = {A probabilistic measure for alignment-free sequence comparison.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/15271780}, volume = {20}, year = {2004} }

TY - JOUR ID - citeulike:552902 L3 - citeulike-article-id:552902 N2 - MOTIVATION: 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). AVAILABILITY: All datasets and computer codes written in MATLAB are available upon request from the first author. IS - 18 JF - Bioinformatics SN - 1367-4803 AD - School of Computing and Information Technology, Griffith University, Nathan Campus, QLD 4111, Australia. t.pham@griffith.edu.au <t.pham@griffith.edu.au> EP - 3461 TI - A probabilistic measure for alignment-free sequence comparison. VL - 20 SP - 3455 KW - alignment-free KW - comparison KW - sequence AU - Pham, TD AU - Zuegg, J PY - 2004/12/12/ UR - http://view.ncbi.nlm.nih.gov/pubmed/15271780 ER -