Video Tip of the Week: Variation Data from Ensembl

Trey introduced me to this “decent collection of video tutorials ” from Ensembl, but he and Mary are currently in Morocco teaching a 3-day bioinformatics workshop & then attending the conference (yes, I am envious!). I am therefore creating this week’s tip based on the tutorials that Trey pointed me to. In today’s tip I am going to parallel a tutorial available from Ensembl on SNP information in order to both: 1) show you haw you can access variation information from Ensembl and 2) compare doing these steps using Ensembl 64 (here in this video) and using Ensembl 54 (archived) (in the Ensembl video).

Bioscience resources often are continuously being developed and improved & it can be difficult to keep videos and documentation up-to-date. That’s why here at OpenHelix we work continuously to keeping our materials up-to-date, with weekly tips on new features and updated tutorials as updated sites become stable.

The Ensembl video (SNPs and other Variations – 1 of 2) is quite nice & provides more detail about the actual Ensembl data than I can in my short movie, but it was done a few years ago on an older version of Ensembl. Since then the resource has been updated, and gone through several new versions of the data. I’m going to follow the same steps that are done in part one of the Ensembl SNP tutorial so that you can see examples of what’s changed & what is pretty much the same. I’d suggest you watch both videos back-to-back to get a good idea of what’s changed, and what types of variation information are available from Ensembl. From that basis I’m sure you’ll be able to watch Ensembl’s second SNP video & apply it to using the current version of Ensembl without much trouble. For more details you can refer to the most recent Ensembl paper in the NAR database  issue, which describes not just variation information but Ensembl as a whole.

Quick links:

Ensembl Browser: http://www.ensembl.org/index.html

Legacy Ensembl Browser (release 54): http://may2009.archive.ensembl.org/index.html

Ensembl tutorial, part 1 of 2: http://useast.ensembl.org/Help/Movie?id=208

Ensembl tutorial, part 1 of 2: http://useast.ensembl.org/Help/Movie?id=211

OpenHelix Ensembl tutorial materials: http://www.openhelix.eu/cgi/tutorialInfo.cgi?id=95

Ensembl Tutorial List: http://useast.ensembl.org/common/Help/Movie?db=core

Reference:
Flicek, P., Aken, B., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Fernandez-Banet, J., Gordon, L., Graf, S., Haider, S., Hammond, M., Howe, K., Jenkinson, A., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Koscielny, G., Kulesha, E., Lawson, D., Longden, I., Massingham, T., McLaren, W., Megy, K., Overduin, B., Pritchard, B., Rios, D., Ruffier, M., Schuster, M., Slater, G., Smedley, D., Spudich, G., Tang, Y., Trevanion, S., Vilella, A., Vogel, J., White, S., Wilder, S., Zadissa, A., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernandez-Suarez, X., Herrero, J., Hubbard, T., Parker, A., Proctor, G., Smith, J., & Searle, S. (2009). Ensembl’s 10th year Nucleic Acids Research, 38 (Database) DOI: 10.1093/nar/gkp972