[Bioperl-l] Gbrowse DAS support

Sean Davis sdavis2 at mail.nih.gov
Wed Feb 25 07:22:35 EST 2004

I have the following situation (and I imagine that I am not unique, here):
I have a number of different oligo and cDNA microarray platforms, each with
probes that have (human) sequence associated with them.  For many of them,
we construct our own annotation by blasting against various databases, the
result being blast results for each probe to genbank sequences, ests, refseq
genes, ensembl genes, or the reference genome.  While this level of
knowledge is adequate for most applications, we are now finding
(particularly with oligo probes) that we need to know with a fair amount of
detail what these sequences look like in genomic context down to the
basepair level.  Therefore, I would like to build a browser that
incorporates my local information including blast hits of my sequence
against various reference sequences.  While I could certainly build a local
database to hold all of the possible references and their assembly, I would
like to use Bio::Das to fetch annotations.  I could see fetching most
annotations from the DAS server, but including tracks for my local data,
also.  And, while I could build a browser, I would like to start with
something done already, and Gbrowse seems a likely candidate for me.

I currently have bioperl-1.4, bio::das, and gbrowse running.  The
installation file for gbrowse says that a feature wish list includes "better
DAS support" and the ability to "configure data sources on a track-by-track"
basis.  Has anyone accomplished this?  Are there other options at which I
should look (including "go do it yourself")?

Sean Davis, M.D., Ph.D.

Postdoctoral Research Fellow

Clinical Fellow

Clinical Fellow, Johns Hopkins
Department of Pediatric Oncology

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