This article will be used to describe strategies to store comparative data within Chado. To kickstart the discussion the ex-TIGR crew will detail their strategy as used in the sybil system. We will discuss/criticize it in the discussion section.
The goal of this article and the ensuing discussion is to define a usage convention for the storage of comparative data in Chado. These data include: Paralogous and Orthologous Gene clusters and Syntenic Blocks (and potentially more?).
See Sybil Chado Comparative Genomics Data to see a description of the Sybil/IGS way of storing comparative data.
This document describes how FlyBase has implemented comparative data for Dmel<->Dpse and also how it plans to implement these analyses for 10 more Drosophila species.
class=”internal” title=”ParameciumDB synteny.pdf”>ParameciumDB</a></span>
ParameciumDB working document heavily inspired by the FlyBase comparative implementation standard. This document describes how ParameciumDB models paralogy and synteny within a genome that has undergone whole genome duplications.