by Peili Zhang, David Emmert, Pinglei Zhou, William Gelbart, and the FlyBase Consortium
The data implementation standard of comparative genomics in Chado is described in this document. The stated data implementation has been formulated by the developers at FlyBase (http://www.flybase.org) and adopted by FlyBase for production. For the purpose of clarity, pairwise comparative genomics results are being employed in this document as examples to illustrate the points. Yet the same implementation can be readily generalized and applied to multiple-genome comparative results. To store the comparative results between two genomes in Chado, the sequence and annotation data of each of the relevant genomes need to be implemented independently in the same Chado database instance. The Chado standards of genomic sequences and annotation are detailed in separate documents, which should be followed before attempting the comparative data implementation described here. Comparative genomics data of interest are grouped into the following two categories: orthology and synteny, for which the Chado standards are illustrated separately below.
Figure 3: Chado representation of syntenic relationship between a pair of genomes, based on orthologous_regions shown in Figure 1. Dmel: Drosophila melanogaster; Dpse: Drosophila pseudoobscura.