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Announcing GO-Figure!

decker at mail.eecis.udel.edu decker at mail.eecis.udel.edu
Fri Mar 22 10:53:29 PST 2002


We are happy to announce the availability for testing of GO-Figure!, 
a tool for the graphical display of the GO annotations, based on
sequence similarity to a query sequence. We presented an early
prototype of this at the Bar Harbor User's meeting last July.

   http://udgenome.ags.udel.edu/gofigure

Given a DNA or protein query sequence, our approach is to use a BLAST
search to identify possible homologs in public databases that have
been annotated with GO terms. These include: SwissProt (SWP), Flybase
(FB), the Saccharomyces Genome Database (SGD), Mouse Genome Database
(MGD) and Wormbase (WB) [1].  The requestor also provides an e-mail
address.  The search will return an email message with a URL link to
three graphs depicting the GO annotations of similar sequences in the
Molecular Function, Biological Process, and Cellular Component
ontologies. 

In the resulting graphs, colored boxes indicate term hits, with darker
color indicating lower E-value. Box shape indicates IEA vs. non-IEA
evidence codes. Colored boxes can be clicked on, and will bring up a
table of all individual database hits and E-values. Links in this
table are functional, and connect back to the original databases.

We are currently using GO-Figure! as one form of display for our
herpesvirus and (soon) chicken genome databases. We are also adapting
it as part of a tool supporting manual GO annotation of gene products
in our databases. Comments and suggestions are welcome.

Dr. Keith Decker             Dr. Carl Schmidt
Salim Khan                   Dept. of Animal and Food Science
Gang Situ                    University of Delaware
Dept. of Computer Science
University of Delaware

-------------
[1] Currently we are using gene ontology terms from the january 2002
release. This will be updated monthly henceforth. Gene products from
MGD, SGD, WB, FB and SWP are from the january 2002 release as well. We
only used EBI's annotations for the human subset within SWP, i.e.
Compugen's annotations have not been used.

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