Tetrahedral Gray Code for Visualization of Genome Information
Identifieur interne : 001A60 ( Main/Curation ); précédent : 001A59; suivant : 001A61Tetrahedral Gray Code for Visualization of Genome Information
Auteurs : Natsuhiro Ichinose [Japon] ; Tetsushi Yada [Japon] ; Osamu Gotoh [Japon]Source :
- PLoS ONE [ 1932-6203 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- genetics : Bees, Genome.
- instrumentation : Computational Biology.
- methods : Computational Biology, Genomics.
- Animals, Color.
Abstract
We propose a tetrahedral Gray code that facilitates visualization of genome information on the surfaces of a tetrahedron, where the relative abundance of each
Url:
DOI: 10.1371/journal.pone.0086133
PubMed: 24475080
PubMed Central: 3903499
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PMC:3903499Le document en format XML
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<term>Genomics (methods)</term>
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<term>Animaux</term>
<term>Biologie informatique ()</term>
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<term>Génome (génétique)</term>
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<front><div type="abstract" xml:lang="en"><p>We propose a tetrahedral Gray code that facilitates visualization of genome information on the surfaces of a tetrahedron, where the relative abundance of each <inline-formula><inline-graphic xlink:href="pone.0086133.e001.jpg"></inline-graphic>
</inline-formula>
-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 <inline-formula><inline-graphic xlink:href="pone.0086133.e002.jpg"></inline-graphic>
</inline-formula>
-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 (<italic>Apis mellifera</italic>
) 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.</p>
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