I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (
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I read about this in Bio-IT World and had to go check it out. It's called the Genome Projector and it has to be the coolest genome browser I've ever seen.
They have 320 bacterial genomes to play with. Naturally, I chose our friend E. coli. The little red pins in the picture below mark the positions of ribosomal RNA genes (It's not perfect, at least one of these genes is a ribosomal RNA methyltransferase and not a 16S ribosomal RNA.)
I'm not entirely happy about finding it now, after I've already written and posted all the assignments for my class, but still, I'll post a link for my students since it's just so cool and it's kind of a neat way to see all the ribosomal RNA genes in one picture.
If you've ever used Google maps, you instantly know how to use this genome browser. You can use the wheel on your mouse to zoom in and out. (Although, there are few problems with controlling the zooming speed.) You can click a mouse button and drag the image from one side to another. And there's a search function for finding specific genes.
The picture below shows the biochemical pathways in E. coli in the spot light and other pathways greyed out.
It's very neat.
And you can see where things map in different ways: within the genome, within a linear map, in a biochemical pathway map, and in something they call a DNA walk map that I don't really understand, but find interesting.
Comments
I was excited to hear about the genome projector on your blog, so I instantly went over to check it out. Having used EcoCyc (http://ecocyc.org/) for browsing the E coli genome I am a bit disappointed. It may look prettier but in terms of content and functionality it is not very useful, particularly for serious work. I think they've a long way to go before they reach the utility of EcoCyc. Over all most of the bioinformatic tools we have are pretty uninspiring and not very creatively done but at least some of them are useful.
Posted by: Herbert M Sauro | March 11, 2008 6:09 PM
I must agree with Mr Sauro, I did not find the projector very useful. The fact that zooming stops before you reach the actual sequence is quite disappointing.
For stunning genome maps I would recommend the Genome Atlas at CBS - http://www.cbs.dtu.dk/services/GenomeAtlas/
Posted by: RF | March 12, 2008 4:51 AM
While its definitely not the best application out there it is a good start for Google, who is just entering the realm of science. Google's participation should be nurtured as their vast resources have a lot to offer.
Posted by: Nicholas Beckloff | March 12, 2008 9:41 AM
@Nicholas: Apart from using the Google Maps API, this project has nothing to do with Google as far as I can see... Anyone can use the Google Maps API for anything they want (obviously, so long as they comply with the License)
Posted by: Tim Yates | March 13, 2008 12:47 PM
The point is that there are very, very few bioinformatics resources that are as easy to use as Google maps. It's very appealing to see people starting to to things like this.
Posted by: Sandra Porter | March 13, 2008 12:55 PM
@Sandra: I completely agree, I was just trying to clear up any confusion, not knock the Genome Projector, or any other "Web 2.0" bioinformatics tools :)
Posted by: Tim Yates | March 13, 2008 6:10 PM