Tag Archives: GeVo

Tip of the Week: CoGe (comparing genomes) revisited

I did a tip on CoGe’s tool, GeVo about two years ago and we’ve had a guest post about CoGe from Eric Lyons, the lead developer of CoGe just over a year ago. In our ongoing and occasional quest to keep our tips fresh (and move them to SciVee), I’ve decided to revisit CoGe and one of their tools. CoGe has changed a bit since we last visited it (see some of the changes here). There is a new interface, more documentation and many more tutorials, some new tools and interconnections and a lot more genomes.  I’m going to give a brief introduction to SynMap and going to use it to do a genome rearrangement analysis (a subject of a text tutorial at the site).ResearchBlogging.org

The algorithm selected in the example is QUOTA-ALIGN which is the subject of a recent paper, “Screening synteny blocks in pairwise genome comparisions through integer programming” in BMC Bioinformatics. As the paper conclusion states:

The QUOTA-ALIGN algorithm screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. These blocks, in turn, may be used for additional downstream analyses such as identifying true orthologous regions in interspecific comparisons.

And as mentioned, and you’ll see in this tip, “QUOTA-ALIGN program is also integrated as a major component in SynMap http://genomevolution.com/CoGe/SynMap.pl webcite, offering easier access to thousands of genomes for non-programmers.
Tang, H., Lyons, E., Pedersen, B., Schnable, J., Paterson, A., & Freeling, M. (2011). Screening synteny blocks in pairwise genome comparisons through integer programming BMC Bioinformatics, 12 (1) DOI: 10.1186/1471-2105-12-102

Tip of the Week: GeVo and Genome Comparison

gevo_thumbToday’s tip of the week introduces a new (to us) tool for genomic comparisons. We came across this tool reading a blog post at James and the Giant Corn (great blog) about a figure from his research proposal. See, there are reasons to read blogs :D. The tool he uses to create this figure and analysis is GeVo at CoGe which has several useful tools in addition to GeVo. In today’s tip of the week, we’ll take a quick look at James’ figure at GeVo and introduce CoGe. Check them out, they look like quite useful tools. (and while you’re at it, check out  James’ blog. Tidbits like this and interesting discussions make it well worth it.)