1. 1. A New Genome Browsing Tool at WormBase Scott Cain scott@scottcain.net WormBase Developer GMOD Project Coordinator
2. 2. Old Genome Browser (GBrowse) Has been around a LONG TIME (it looks a little like the 90s). Can have issues dealing with newer data types (no support for VCF, BAM can be quite slow). Has reached end of development. Considerable hassle to maintain.
3. 3. New Genome Browser (JBrowse) Next Gen genome browser in the GMOD project. Uses JavaScript/AJAX to provide a very interactive, speedy experience. Image rendering takes place in the web browser rather than on a server (speedy for you, smaller servers for us).
4. 4. Navigation (show movie)
5. 5. Data Manipulation File menu Open (local/remote) Combination Tracks Sequence Search
6. 6. Open Supports BAM, BigWig/Bed, Indexed VCF and GFF3 Supports local open, i.e., it will open files without uploading them to a server (so it is FAST) Fetching by URL from web/ftp (so can use Google Drive, DropBox, etc)
7. 7. Combination Tracks After selecting Create Combination Track, simply drag the two tracks together that you want to combine. Use set operations to combine (intersection, union, subtraction, etc)
8. 8. Sequence Search Create a persistent track that will show you when reference sequence matches a pattern. Can be strand specific Can use regular expressions Can search DNA or translated amino acid sequence
9. 9. Other Niceties Pin to top makes a track sticky at the top (wont scroll away) Download track data Create a URL that you can email, post, etc. Full page button removes WormBase header/footer giving you the whole web page for genome browsing.
10. 10. Wrap up Much thanks to Ian Holmes (UC Berkeley) and his group, particularly Rob Buels, and Colin Diesh in Chris Elsiks group (U Missouri). Poster 953A (Thursday, 9:00-10:30PM) The new genome browser is available at http://jbrowse.wormbase.org/ (redirects to main WormBase site). I tend to hang out on IRC (##worms and #gmod at freenode.net), and of course you can always send email to help@wormbase.org or me directly at scott@scottcain.net. PLEASE feel free to make suggestions for improvements!