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Talk:GBrowse Configuration/DAS

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Test transclusion


Using DAS (Distributed Annotation System) Databases

You may insert features from a DAS source into any named track. Create a stanza as usual but instead of specifying the feature type using the "feature" option, give the desired DAS URL using the "remote feature" option:

remote feature = http://dev.hapmap.org/cgi-perl/das/t2d_testing?type=ldblock

Because DAS sources specify the glyph and visualization options, most of the settings such as bgcolor will be ignored. However, the track key and citation options are honored.

You can use the same syntax to load a GFF file or a feature file in Gbrowse upload format into a track. Just provide a URL that returns the desired data.

You can also run GBrowse entirely off a single DAS source. To get this support, you must use Bio::Das version 0.90 or higher, available from http://www.biodas.org.

A sample [GENERAL] configuration section looks like this:

[GENERAL]
description   = Das Example Database (dicty)
db_adaptor    = Bio::Das
db_args       = -source http://www.biodas.org/cgi-bin/das
                -dsn    dicty

The db_adaptor option must be set to "Bio::Das". The db_args option must contain a -source pointing to the base of the remote DAS server, and a -dsn pointing to the name of the annotation database.

The remainder of the configuration file should be configured as described earlier. The following short script will return a list of the feature types known to the remote DAS server. You can use the output of this script as the basis for the tracks to configure.

 #!/usr/bin/perl
 
 use strict;
 
 use Bio::Das;
 my $db = Bio::Das->new('http://localhost/cgi-bin/das'=>'dicty');
 print join "\n",$db->types;

Limitations:

The DAS implementation does not descend into subcomponents. For example, if the user requests features on a chromosome, but the remote DAS server has annotated genes using contig coordinates, then the genes will not appear on the chromosome.

The gbrowse_details script does not provide useful information because the DAS/1 protocol does not provide a way to retrieve attribute information on a named feature.