title: Similarity Estimation Between DNA Sequences Based on Local Pattern Histograms of Binary Images.
abstract: Graphical representation of DNA sequences is one of the most popular techniques for alignment-free sequence comparison. Here, we propose a new method for the feature extraction of DNA sequences represented by binary images, by estimating the similarity between DNA sequences using the frequency histograms of local bitmap patterns of images. Our method shows linear time complexity for the length of DNA sequences, which is practical even when long sequences, such as whole genome sequences, are compared. We tested five distance measures for the estimation of sequence similarities, and found that the histogram intersection and Manhattan distance are the most appropriate ones for phylogenetic analyses.
authors.affiliation: Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan.
authors.forename: Yusei
authors.initials: Y
authors.lastname: Kobori
authors.affiliation: Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan. Electronic address: slmizu@hirosaki-u.ac.jp.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Mizuta
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D054629:Genome, Mitochondrial / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
keywords: Bitmap image; Distance measure; Genome sequence; Mitochondria; Occurrence frequency