Variant viewers are very popular. As we get more and more sequence data, the challenge of looking across many samples only gets more and more important. So I always like to see how different groups are doing this. I’m still waiting for the killer app on this–the pan-genome graphs with all the paths along different genomes/regions displayed. But there are many good examples out there now for seeing variations in different species, strains, or different individuals.
This week’s Video Tip of the Week looks at the yeast variation viewer from SGD. It shares some features with other visualization tools (lollipops are hip, lately). But it has a very quick way of switching back and forth from DNA to protein that isn’t always available on variation viewers that I’ve tried before.
So this week’s video tip shows you their quick tour of their recently added variant viewer tool.
I won’t go into any more detail–they have a whole paper in the NAR database issue 2016 that describes the development and the features (below). Go over and try it out, it’s speedy and easy to use.
Cherry, J., Hong, E., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E., Christie, K., Costanzo, M., Dwight, S., Engel, S., Fisk, D., Hirschman, J., Hitz, B., Karra, K., Krieger, C., Miyasato, S., Nash, R., Park, J., Skrzypek, M., Simison, M., Weng, S., & Wong, E. (2011). Saccharomyces Genome Database: the genomics resource of budding yeast Nucleic Acids Research, 40 (D1) DOI: 10.1093/nar/gkr1029
Sheppard, T., Hitz, B., Engel, S., Song, G., Balakrishnan, R., Binkley, G., Costanzo, M., Dalusag, K., Demeter, J., Hellerstedt, S., Karra, K., Nash, R., Paskov, K., Skrzypek, M., Weng, S., Wong, E., & Cherry, J. (2016). The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Research, 44 (D1) DOI: 10.1093/nar/gkv1250