Tetrahedral gray code for visualization of genome information.
We propose a tetrahedral Gray code that facilitates visualization of genome information on the surfaces of a tetrahedron, where the relative abundance of each [Formula: see text]-mer in the genomic sequence is represented by a color of the corresponding cell of a triangular lattice. For biological significance, the code is designed such that the [Formula: see text]-mers corresponding to any adjacent pair of cells differ from each other by only one nucleotide. We present a simple procedure to draw such a pattern on the development surfaces of a tetrahedron. The thus constructed tetrahedral Gray code can demonstrate evolutionary conservation and variation of the genome information of many organisms at a glance. We also apply the tetrahedral Gray code to the honey bee (Apis mellifera) genome to analyze its methylation structure. The results indicate that the honey bee genome exhibits CpG overrepresentation in spite of its methylation ability and that two conserved motifs, CTCGAG and CGCGCG, in the unmethylated regions are responsible for the overrepresentation of CpG.
Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, Japan.
Natsuhiro
N
Ichinose
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology (KIT), Kawazu, Iizuka, Fukuoka, Japan.
Tetsushi
T
Yada
Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo, Japan.
Osamu
O
Gotoh
D000818:Animals; D001516:Bees / Q000235:genetics; D003116:Color; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods*; D016678:Genome / Q000235:genetics*; D023281:Genomics / Q000379:methods*