More as an educational than a research tool, I'd like to give a presentation on human genetics using a human genome browser that can start at the single-base level, and zoom (smoothly if possible) out to the entire chromosome. The catch is that I won't have internet access when giving the presentation. I'm happy to download reference sequences, annotations, etc. The main things I'd like to display are (at the fine scale) intron/exon positions, and at the wider scale, gene positions, alu/SINE positions, and (if possible) simple gene repeats such as human MW/LW opsins. I like http://chromozoom.org, but it's hard to get working offline. I find that http://www.biodalliance.org doesn't have a terribly nice chromosome-wide view. Are there others that people could suggest?
5 answers
Integrated Genome Browser [IGB] may be what you are looking for. We used to use this for research as well but at the time it did not scale well for large datasets (I have not performance tested it recently though)
Integrative Genomics Viewer [IGV] is what we use at the moment for research but it might not look as slick for your intended audience.
Both genome browsers can work offline with local files (e.g. bed format).
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Alastair Kerr
When talking about zooming into the genome. IGB is really good indeed.
I haven't played around with it too much, but GoldenHelix's genome browser might be something to check out. http://www.goldenhelix.com/GenomeBrowse/index.html
Look at the new UCSC genome browser in a box. You set it up on your local machine, and then you can use it just like a connected browser, with a couple of minor exceptions.
http://blog.openhelix.eu/?p=20193
You can pick the tracks you want.
The other great thing is that students who go to UCSC later will be able to do all the same stuff on their own with very little overhead. They can use the web site and replicate some of what you show. A totally custom one you create just for this, they can't do that.
Neat-o, thanks!
Genomorama (http://public.lanl.gov/jgans/genomorama/) offers offline, smooth zooming from the base to the chromosome scale. It can read GBK files for sequence and annotation data. Panning and zooming can be controlled by the mouse and/or keyboard.
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This is probably not something you can easily use right now. But here is something I worked on last year, but never finished. Here is a demo showing human chromosome 1: http://www.nextgenetics.net/tools/browser/browser.html
And it is pure javascript/html so it is offline-able. The github is here: https://github.com/damiankao/seeker.
Use the AWSD keys to move around and Q and E to zoom in/out. You can try to zoom out on human chromosome 1, but you will eventually crash your browser (way too many elements to try to visualize at once).
I am trying to make it into a simple browser for viewing annotations. Here is a version with more UI components I did over Christmas break: http://nextgenetics.net/sequitur/browser.html
I am working on the backend with node.js right now.