1. A New Genome Browsing Tool at WormBase Scott Cain
[email protected] WormBase Developer GMOD Project
Coordinator
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. 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. Navigation (show movie)
5. Data Manipulation File menu Open (local/remote) Combination
Tracks Sequence Search
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. 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. 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. 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. 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 [email protected] or me directly at
[email protected]. PLEASE feel free to make suggestions for
improvements!