BCM Sequence Annotation Web Server

Randall Smith rsmith at DOT.IMGEN.BCM.TMC.EDU
Mon Aug 22 16:47:23 EST 1994


   Announcing a new WWW Server: The BCM Sequence Annotation Server

URL:  http://dot.imgen.bcm.tmc.edu:9331/seq-annot/home.html

Developed by Kanwal Gill, Brent Wiese, and Randall Smith
Human Genome Center, Baylor College of Medicine, Houston TX  USA


We have created a "Sequence Annotation" WWW Server that allows
researchers to add their own annotations to Entrez (NCBI) DNA and
protein sequence reports.  Our Annotation Server is intended as a
method for investigators to easily share new information about
sequences, e.g., new features, interesting sequence matches, domain
identifications, etc.

A user who wishes to make an annotation for an Entrez sequence will be
given the chance to select an annotation type (eg coding region,
variant, etc.). The user is then requested to enter a short annotation
that will appear as an embedded link in an Entrez report.  The
annotator will then be prompted to enter an extended commentary which
gives the further details about the annotation. The annotator may also
enter some keywords that can be searched on and URL's that will lead
to more information (eg, an entry in another database, a file of data
on the annotator's home computer, etc).

Only the annotations themselves are stored on our local server. When a
user wishes to view an annotated record, our server requests a
sequence report from the NCBI Entrez Server. The local annotations are
then embedded within the returned report.

As an initial entry, we have added several hundred annotations based
on data kindly provided by Keith Robison.  The annotations list
probable coding regions within bacterial sequences that are not
annotated as such in GenBank (see Table 2 of K. Robison, W. Gilbert
and G.M. Church, "Large scale bacterial gene discovery by similarity
search", Nature Genetics 7:205, 1994).

We invite the biological community to use the server to view this data
as well as to add data of their own.  Users wishing to view the data
need only the URL listed above and a graphical WWW browser such as
Mosaic or Chimera.  Users wishing to add data would be well-advised to
also prepare the text of their annotation and extended commentary as
well as to have their URL's (if any) in mind before beginning.
Extensive on-line help is provided for both types of users.

Suggestions and comments regarding how the server can best meet the
needs of the biological community are welcome.  There is a comments
form provided in the server for typing in your comments.  Comments may
also be emailed to Randall Smith at rsmith at bcm.tmc.edu.



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Randall F. Smith
Human Genome Center
Department of Molecular and Human Genetics and
W.M. Keck Center for Computational Biology
Baylor College of Medicine
Houston, TX  77030  USA

rsmith at bcm.tmc.edu
713-798-4735; FAX: 713-798-5386
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