Tag Archives: map viewer

If you hadn’t noticed, it’s the Year of the Rats

ratMary pointed out (and I’ve Tivo’d for my daughter, the great lover of rats) that the History channel had a special on rats recently. Well, not to be outdone, Nature Genetics May issue is all about rats. There are some great articles in that issue about rat genetics and rat genetics as a model for human disease genetics. And if you are at all interested in Rat genomics, the article “What everybody should know about the rat genome and it’s online resources” is a very useful read (and freely accessible I believe). The article will walk you through some of the rat genome data and tools available at Ensembl, NCBI, UCSC Genome Browser and RGD *. Definitely worth checking out.

Now, History channel specials and Nature Genetics focuses have set the bar high for next year’s Year of the Ox, the bovine genome was completed last year.

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Happy DNA Day!

dna dayWatson and Crick’s discovery was 55 years ago (original Nature article). The Human genome was completed 5 years ago.

And thus DNA Day every April 25th in celebration of those two huge milestones. The celebrations often revolve around education and educational tools to teach students, scientists and the public about the science behind DNA and the genome.

As we mentioned last week (that post has more interesting information about DNA Day), we are celebrating here too. Well, actually we celebrate DNA day every day ;), it’s our job.. but in extra celebration…

We are offering a tutorial on how to use the NCBI Map Viewer. The NCBI Map Viewer, as our blurb says,

organizes and displays dozens of species genomes, and provides additional context with appropriate annotations for the genomic sequences. Extensive integration with other NCBI tools enables researchers to link quickly to relevant additional details.mapviewer

So, go check it out and learn a little more in celebration of DNA Day! (and don’t forget, there are 7 free full tutorial suites available)

Also, DNA Day is begin celebrated around the world, check out some of these celebrations:

At “Eye on DNA” points to a DNA Day ECard!

Go to the DNA Day Chat Room at the National Human Genome Research Institute

Go extract your own DNA or “write your name in DNA” in beads of four colors for the real DNA geek in you.

Read some “Reflections on DNA Day” at SEA.

Linking phenotypes and genotypes.

Ok, that’s a really broad title for an important area. And it is a problem that we are starting to see addressed more and more with GWAS (genome wide association studies). ResearchBlogging.org If you came here hoping that I had solved this, I’m sorry to disappoint you. We are asked all the time for places to look for this kind of information. The relatively new “Phenotypes and Disease Association Tracks” on the human UCSC Genome Browser have been popular in the training sessions we have given (look at the human browser, and check the second group of tracks controls on the page). You can find OMIM data in Ensembl. You can add Morbid Map to your Map Viewer. Another resource that I just found out about is trying to get at the same types of data–but it is available from their interface and also on the HapMap browser.

MutaGeneSys is a tool with a very simple interface at their web site, but the data is also displayed as a track in the GBrowser at HapMap. The goal was to combine HapMap information + OMIM + whole-genome marker correlation data. The news page at HapMap that describes the addition of this track to HapMap says:

Predicted OMIM associations available in GBrowse

The OMIM associations track presents data from the MutaGeneSys database, which links genotype data from HapMap and whole genome association studies with the known disease variants reported by the OMIM database. Example of a region with multiple OMIM associations: Chr1:194923128..194933127

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