A probabilistic measure for alignment-free sequence comparison

Pham T.D. and Zuegg J. (2004) A probabilistic measure for alignment-free sequence comparison. Bioinformatics, 20 18: 3455-3461. doi:10.1093/bioinformatics/bth426

Author Pham T.D.
Zuegg J.
Title A probabilistic measure for alignment-free sequence comparison
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1367-4803
Publication date 2004-12-12
Sub-type Article (original research)
DOI 10.1093/bioinformatics/bth426
Volume 20
Issue 18
Start page 3455
End page 3461
Total pages 7
Language eng
Subject 1308 Clinical Biochemistry
1703 Computational Theory and Mathematics
1706 Computer Science Applications
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).
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
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