Predicting Genes and Comparing Viral Genomes

Example 2

Genes were predicted using Gene Locator and Interpolated Markov ModelER (Glimmer)³⁸. For each sequenced genome, protein sequences of known genes of the respective reference from GenBank were aligned with exonerate³⁹ to the assembled genome sequence. The coordinates of the best hits were then used to build a Glimmer model which was subsequently used for prediction of location and orientation of genes in the sequenced genome.

Next, protein sequences were compared between virus genomes. The result of this analysis is given in FIG. 6. Shown are genome organisations for 28 sequenced human adenoviruses. Genes and their orientation are shown as gray-shaded shapes on both strands of the genome (solid line). All genomes show the canonical organization of the Mastadenovirus genus.

Shading of a gene reflects its maximum sequence divergence across all 28 viruses determined through an all-vs-all Blast analysis.