Advanced Relation Model for Genome Sequence Visualization (ARM 4 GSV): Exploratory Visualization Examples

The Advanced Relation Model for Genome Sequence Visualization (ARM 4 GSV) is proposed in this paper. This model is adapted from an earlier visualization model which has been applied to the visualization of computer programs. A review of the fundamental model components of the earlier visualization model is given. Enhancements so as to make it applicable in genome visualization are discussed. As part of these enhancements, a relational characterization of genome sequences in terms of bases, codons, and patterns such as close inversions is developed and described. An adapted form of the Conceptual Crown Visualization (CCV) model, a part of the earlier work, is discussed. Applications of the ARM 4 GSV to codon usage distribution and close inversion distribution are discussed. These applications are accompanied by many visualization figures of a 269 base RNA molecule, a part of the Hepatitis C virus NS5 gene, Locus AY769711. Our presentation illustrates the extent and flexibility of our approach. We conclude by observing that our objectives of showing the potential usefulness of our proposed visualization model are met.