A New Graphical Representation of DNA Sequences Using Symmetrical Vector Assignment

Kyohei Yamaguchi ； Satoshi Mizuta

《Review of Bioinformatics and Biometrics》 3卷 (2014/12) Pp. 14-21

並列摘要

Analyzing the similarities between genomic sequences is one of the principal methods used to investigate the evolutionary relationships between species. For relatively short sequences, such as nucleotide sequences of genes or amino acid sequences of proteins, alignment is widely used to evaluate the sequence similarity. However, the alignment is not practical for comparing very long sequences, such as genome sequences, due to its time-consuming nature. In this article, we propose a new method for graphical representation of DNA sequences, which falls into one of the major categories of alignment-free sequence comparison. We introduce a practical method for the numerical conversion of DNA sequences, in which we assign three-dimensional vectors in a symmetrical manner to the bases of genome sequences. We confirm the usefulness of our method in terms of the intuitive assessment of sequence similarities.

並列關鍵字

Alignment-free ； Sequence Comparison ； Mitochondrial Genome ； 3D Graph