Tag Archives: CMap

DragonDB? Who knew….

snapdragonNow, I like to immerse myself in databases–including some pretty obscure species.  But even I had no idea there was a dragon database.

Snapdragon!  http://www.antirrhinum.net/

I’m working on an update for our Gramene tutorial right now, so I’m all over plant resources and following some links today I found the dragon.  There are some other ones I need to check out as well–from the Gramene link to VPIN, the Virtual Plant Information Network.

The Legume Information System was new to me as well.  I’m a big fan of legumes, as they constitute a huge portion of my protein sources.  There was also a link to SoyBase, which also has a soybean breeder’s toolbox.  I see their genetic map is in CMap, which is in that list of GMOD tools I mentioned the other day, and is also used by Gramene.   These tools are popping up all over the place–and if you learn to use them in one place you can usually transfer those skills to other species of interest as they come along.

GMOD summer school–homework!

Well, ok, you aren’t required to do the homework–it’s just available for you if you want to work on setting up GMOD tools around your projects (or at home, if you want…).

We mentioned that the GMOD summer school was going on, and now that it’s all successfully wrapped up many of the materials are available as tutorials on the GMOD site: http://gmod.org/wiki/Training_and_Outreach

These are mostly installation and configuration tutorials for the software components.  Although the end user tutorial we created for GBrowse is in the list as well–the emphasis is definitely on developers.

The tools included in this tutorial collection are all pieces of the GMOD suite.

  • Apollo, a genome annotation editor.
  • BioMart, a data mining system that lets you build complex queries from the underlying databases.
  • Chado,relational database underlying the GMOD tools.
  • CMap, comparative genomics tool for viewing maps
  • GBrowse, a genome browser used at for many species.
  • MAKER, genome annotation pipeline.
  • Tripal, a front-end to Chado databases.

As more and more people get next-generation sequencing data for their species of interest these tools and support for them will be increasingly crucial.