Display CMap Markers in GBrowse

This proposal came out of a presentation by Erick Antezana and Frederic Potier at the August 2009 GMOD Meeting titled:

• GBrowse: Lessons Learned and Statement of Interest

From Frederic and Erick:

We were thinking about having CMap features displayed in GBrowse in one or more dedicated tracks. Using now the fact that GBrowse can be connected to multiple datasources, the GBrowse config file could be for example:

<perl>#################################

1. database definitions
2. Database for genome annotations.

[GGB_TIGR_RICE_V5:database] db_adaptor = Bio::DB::GFF db_args = -adaptor dbi::mysql

   -dsn dbi:mysql:GGB_TIGR_RICE_V5:localhost:3306
   -user ...
   -pass ...

1. Database for NGS

[bamtest:database] db_adaptor = Bio::DB::Sam db_args = -fasta sequence.fasta

                 -bam   bam_file.bam

1. Database for genetic markers

[CMAP_TIGR_RICE_V5:database] db_adaptor = specific CMAP adaptor or maybe an already existing one  ??? db_args = -adaptor dbi::Oracle

   -dsn dbi:Oracle:CMAP_TIGR_RICE_V5:localhost:
   -user ...
   -pass ...

...

1. 1. 1. TRACK CONFIGURATION ####

...

[Pair] feature = read_pair glyph = segments database = bamtest draw_target = 1 show_mismatch = 1 bgcolor = sub {

                     my $f = shift;
                return $f->get_tag_values('M_UNMAPPED') ? 'red' : 'green';
              }

fgcolor = green height = 3 label = sub {shift->display_name} label density = 50 bump = fast connector = dashed key = Read Pairs

[AFLP_RICE] feature = aflp database = CMAP_TIGR_RICE_V5 map_set = tigr_rice_v5 key = CMAP AFLP markers category = Molecular Mapping

[SSR_RICE] feature = aflp database = CMAP_TIGR_RICE_V5 map_set = tigr_rice_v5 key = CMAP SSR markers. category = Molecular Mapping .... </perl> As you can see, both AFLP_RICE and SSR_Rice are pulled out from the CMap database and displayed in dedicated tracks.

Then the idea is to manage the links to CMap via an url in the popup ballon.

This configuration should be very convenient to integrate CMap/GBrowse without requiring a lot a maintenance and administration.