Tag Archives: Apollo

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.

Ok, say you get a genome. What next?

There may be a lot of opportunity to get one’s genome of interest sequenced in the near future.  And I don’t only mean your own personal genome–I mean your species of interest.  There should be academic centers and service providers who offer genome sequencing at increasingly reasonable pricing soon.

So let’s say you get your favorite sample done: what next?  We have talked about how cool it is to be able to use the GBrowse or WebGBrowse tools to display your data.  But that is missing a step, actually.  To get appropriate data to display you need to annotate your genome.  You need to curate your genome.  The GMOD suite offers some tools to do this–Apollo can be a part of your strategy. JCVI has an annotation service for prokaryotic genomes that uses Manatee. They frequently offer a prokaryotic annotation course around that process as well.

But the other day I heard about another option that I thought I would mention: the BLAST2GO team is announcing a course on Automated Functional Annotation and Genome Mining.  Here is their announcement via the GOFriends mailing listpersonally I would choose the one in Valencia :)


•Are you working in sequencing projects?
(EST projects, Next Generation Sequencing, Microarray desing, etc… )
•Do no have thousands of novel sequences that need functional annotation?
•Do you need a user-friendly tool to functionally analyze your data?
The Blast2GO Team is very pleased to announce:


In this course you will learn tools and tips for functional
annotation, visualization and analysis of novel sequence data making use of Blast2GO.

The course will be offered to 35 participants at 2 locations:
•Valencia, Spain: 28 to 30, September 2009
•Florida, USA: 14 to 16, October, 2009
For more information and registration until the 1 of September please visit:

But Florida in October wouldn’t be a bad option either!

For more information about just the BLAST2GO part, check out this site: http://blast2go.org/