Tag Archives: genome evolution

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: Genomicus and genome evolution

ResearchBlogging.orgToday’s tip is on Genomicus. Genomicus is a great tool to visualize gene duplication, synteny and genome evolution. The search and display interfaces are quite straightforward, and there are lots of great features (viewing ancestral gene information, links out to resources, different views of phylogenies, etc) in the tool. This video is only a short introduction. You can delve deeper into the tool with the help and documentation, including an 11 minute video.

There is also a recent (advance access) paper in the journal “Bioinformatics” that will give you a lot more detail on how the database and tool works and what is there.

Muffato, M., Louis, A., Poisnel, C., & Roest Crollius, H. (2010). Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes Bioinformatics DOI: 10.1093/bioinformatics/btq079

You will also notice today the video is a SciVee embed. We are trying out a new way to post and share our tips. SciVee allows us to not only post on our blog, but for you to share the tip with others and also for scientists in the SciVee community to view the tips. This is only a test. We will be working with this for the next couple weeks to find the best way to post and share. Eventually, soon, we hope to share these on Facebook and Youtube also. If the video is not high enough quality for you (SciVee and other video sharing sites by necessity reduce size, you can try out the entire mpeg4 version a this link.