As you may know, we’ve been doing these video tips-of-the-week for FOUR years now. We have completed around 200 little tidbit introductions to various resources from last year, 2011 (yep, it’s 2012 now). At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.
VISTA has added a couple of new features to their great comparative genomics resource, dot plots and synteny browser. They are excellent features and additions, but they are not yet easy to find from the homepage. Today’s tip I’m going to show you where they are and take a quick look at what they do. If you want to look at comparative genomics and synteny, you’ll want to check out this feature. They linked from Vista-Point (which was added early last year), which you can learn more about in the open-access tutorial here. To learn more about what they do and how to use them, check out the VISTA help section linked here.
Today’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.
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.