Similarity Estimation Between DNA Sequences Based on Local Pattern Histograms of Binary Images
- Author:
Kobori YUSEI
1
;
Mizuta SATOSHI
Author Information
1. Graduate School of Science and Technology
- Keywords:
Genome sequence;
Mitochondria;
Bitmap image;
Occurrence frequency;
Distance measure
- From:
Genomics, Proteomics & Bioinformatics
2016;14(2):103-112
- CountryChina
- Language:Chinese
-
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.
