Tip of the Week: Plant comparative genomics using Plaza

ResearchBlogging.orgPlaza, a resource for plant comparative genomics, has a lot more than meets the eye at first. Currently the database has comparative tools and data for nearly 2 dozen plants including monocots, dicots, mosses and algae. There are some obvious tools and data from the homepage, but I suggest you take a look at the documentation and tutorials, you’ll find there is a lot more once you start delving into it. In this tip, I’m going to walk though getting phylogeny of a gene family from a specific clade to illustrate that there is a lot here that you might not see at first.

Plaza: http://bioinformatics.psb.ugent.be/plaza/

For grass comparative genomics you might also want to check out Gramene (tutorial, subscription) and for general comparative genomics, VISTA (tutorial, free) is an excellent resource also.

Proost, S., Van Bel, M., Sterck, L., Billiau, K., Van Parys, T., Van de Peer, Y., & Vandepoele, K. (2009). PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants THE PLANT CELL ONLINE, 21 (12), 3718-3731 DOI: 10.1105/tpc.109.071506