What’s the Answer? (zoomable browser)

Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.

This week’s highlighted question hits on something I’ve mused about before. We could really use some more lightweight browsing tools that are more consumer-level appropriate. Although I think there are some tools to accomplish various different things that sophisticated end users could work with. But there’s still a gap, which I still think would be a great project for some student team.

The extra wrinkle on this question, though, is it needs to be able to run without an internet connection.

Question: Any good offline zoomable genome browsers?

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?

hyanwong

If you have some suggestions, please bring ‘em along. This question pops up on a somewhat regular basis, and we could really use more ideas on this.