title: Measurement of word frequencies in genomic DNA sequences based on partial alignment and fuzzy set.
abstract: Accompanied with the rapid increase of the amount of data registered in the databases of biological sequences, the need for a fast method of sequence comparison applicable to sequences of large size is also increasing. In general, alignment is used for sequence comparison. However, the alignment may not be appropriate for comparison of sequences of large size such as whole genome sequences due to its large time complexity. In this article, we propose a semi alignment-free method of sequence comparison based on word frequency distributions, in which we partially use the alignment to measure word frequencies along with the idea of fuzzy set theory. Experiments with ten bacterial genome sequences demonstrated that the fuzzy measurements has the effect that facilitates discrimination between close relatives and distant relatives.
authors.affiliation: Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan.
authors.forename: Fumiya
authors.initials: F
authors.lastname: Shida
authors.forename: Satoshi
authors.initials: S
authors.lastname: Mizuta
mesh_terms: D019609:Archaeoglobus / Q000235:genetics; D001407:Bacillus / Q000235:genetics; D048168:Escherichia coli K12 / Q000235:genetics; D019453:Escherichia coli O157 / Q000235:genetics; D017143:Fuzzy Logic; D016678:Genome; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D010802:Phylogeny; D043902:Pyrococcus horikoshii / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014734:Vibrio cholerae / Q000235:genetics; D015010:Yersinia pestis / Q000235:genetics
keywords: Alignment-free; linguistic approach; rank correlation