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Add new DAS URLs, some old ones didn't work

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Brian O
Brian O committed Mar 22, 2007
1 parent 673c79d commit e4bf46112b936e95c340bd11fb8304796d619d7a
Showing with 11 additions and 21 deletions.
  1. +11 −21 docs/pod/DAS_HOWTO.pod
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@@ -5,14 +5,9 @@ protocol for sharing and integrating genomic annotations. GBrowse can
act both as a DAS front end for visualization and as a DAS server for
sharing your annotations.
For a good introduction to the DAS features of GBrowse, see the online
tutorial at http://www.gmod.org/ggb/tutorial/tutorial.html#DAS. This
document is a concise reference to the DAS integration features.
You will need to install the Perl Bio::Das module before you can use
any of the DAS features. This module is available from CPAN
( http://www.cpan.org ), or via the ActiveState PPM tool in the
repository http://www.gmod.org/ggb/ppm .
(L<http://www.cpan.org>), or via the ActiveState PPM tool.
=head2 CONFIGURING GBROWSE TO BE A DAS SERVER
@@ -123,30 +118,25 @@ errors.
You can display individual DAS tracks in GBrowse just by typing in the
URL of a DAS server in the "Add remote annotations" section of the
GBrowse main web page. The syntax of the URL is simple:
GBrowse main web page. The syntax of the URL is simple - some examples:
=over 4
=item http://genome.cse.ucsc.edu/cgi-bin/das/hg16
Insert all features defined in database hg16 (human genome release
from July 2003) from the DAS server located at genome.cse.ucsc.edu.
=item http://genome.cse.ucsc.edu/cgi-bin/das/hg16?type=genscan
=item http://www.wormbase.org/db/das/elegans/features?segment=I
Insert all features of type "genscan" from the UCSC database.
Insert all features of C. elegans chromosome I
=item http://genome.cse.ucsc.edu/cgi-bin/das/hg16?type=genscan;type=mgcFullMrna
=item http://www.wormbase.org/db/das/elegans/features?segment=I:1000,2000
Insert all features of type "genscan" and of type "mgcFullMrna."
Insert all features of a given segment of C. elegans chromosome I.
=item http://genome.cse.ucsc.edu/cgi-bin/das/hg16?category=variation
=item http://www.wormbase.org/db/das/elegans/features?segment=I:1000,2000;category=SAGE_tag:SAGE_tag_genomic_unique
Insert all features of category "variation."
Insert all unique SAGE tags from the given segment of chromosome I.
=item http://genome.cse.ucsc.edu/cgi-bin/das/hg16?category=variation;type=genscan
=item http://genome.cse.ucsc.edu/cgi-bin/das/hg18/types
Insert all features of category "variation" or of type "genscan."
Insert all known types in human genome build 18.
=back
@@ -196,4 +186,4 @@ Details can be found at http://www.biodas.org/
=head1 AUTHOR
Lincoln D. Stein, lstein@cshl.edu
Lincoln D. Stein, lstein@cshl.edu

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