For this month, the focus is on enhanced comparative functionality within and outside the legumes
by means of our partnerships in the Legume Federation.
Our InterMines now use the "friendly mine" capabilities of Intermine to interlink our own mines together with
one another and with mines maintained by other groups; e.g. ThaleMine, for a wealth of information
on Arabidopsis thaliana orthologs to the legume genes maintained in our mines. For those species
currently stored in the mines (Medicago truncatula, Glycine max, Phaseolus vulgaris, and the diploid Arachis species),
their LegumeMine gene pages are now directly accessible from the link menus in our phylogenetic trees and our genome
context views. For example, try going to this tree and click on the highlighted gene from "phavu" (common bean).
Choose the LegumeMine link in the menu that appears and then look through the details integrated into the report page,
including the spanning QTLs of the gene. Then check the "Links to other Mines" on the right hand side for further
information about the orthologs.
Our Genome Context app now serves genomic data to federated versions of the viewer. A federated viewer
consuming this service, and supplying data for selected outgroup species (currently Arabidopsis
thaliana, and four non-legumes from the Fabidae) is now hosted by the Legume Federation, allowing
exploration of syntenic relationships across longer evolutionary distances. For example, this set
using Arabidopsis as the query track (note the segmental duplication present in Arabidopsis chromosome 5).
If you're interested in hosting your own genomes and providing services that can be federated with others
like ours, check out the Genome Context Viewer code repository
and contact us if you need any assistance getting started.