[Genome] Adding a new genome (or genomes) to the public site

[Donna Karolchik]

hi Roger,

As you have probably noticed, we've restricted the genome assemblies available 
on the Genome Browser to vertebrates, a collection of flies, and a few other 
model organisms. At this point, we have no plans to add bacteria to the UCSC 
Genome Browser site. However, you may want to contact the Todd Lowe lab at UCSC, 
who have adapted the Genome Browser to display Archae and extremophiles. Their 
browser is available at http://archaea.ucsc.edu. You'll find contact information 
at the bottom of that web page.

-Donna
-----------------------------------
Donna Karolchik
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

----- Original Message ----- 
From: "Roger Bumgarner" <rogerb at u.washington.edu>
To: <genome at soe.ucsc.edu>
Cc: "Weerayuth Kittichotirat (AKA Kai)" <kitticho at u.washington.edu>
Sent: Friday, October 27, 2006 2:53 PM
Subject: [Genome] Adding a new genome (or genomes) to the public site


> All,
>
> We are working on some comparative genomics projects looking at
> different strains of Actinobacillus actinomycetemcomitans.  At
> present there is a single strain that has been sequenced and which is
> in the public domain but we've recently produced a nearly complete
> sequence of a 2nd strain and will do a third soon.  We'd like to use
> Genome Browser to display the various strain relative to each other
> and to display annotation of a variety of sorts as part of out
> comparative analysis.  While I understand that we can download
> GenomeBrowser locally and add both new genomes and whatever track we
> wish, I was also wondering what UCSC's policy/process is regarding
> adding new genomes to your public site.  My thought is that we will
> eventually want to publish our comparative genomics analyses and will
> want to make much of our results available and visualizable via the
> Genome Browser.  Is that best accomplished by:
>
> 1) Convincing someone at your place that it's worthwhile to add the
> AA genome to your site?
> 2) Setting up a second public site at our location which is focussed
> on AA?
>
> Your advice/thoughts/constraints on such an endeavor would be
> appreciated.
>
> With best regards,
>
> Roger E. Bumgarner
> Associate Professor
> Mailing Address (for US Post ONLY):
> Department of Microbiology, Box 358070
> University of Washington
> Seattle WA 98195
>
> Shipping Address (for packages, FedEx, UPS, DHL etc.):
> 960 Republican St.
> Seattle WA, 98109
>
> Phone
> (206)732-6137(voice)
> (206)732-6055(fax)
> (206)790-5496 (mobile)
> http://expression.washington.edu/bumgarnerlab
>
>
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