On Nov 1, 2006, at 4:03 PM, Jonatha Gott wrote:
Hi all,
Sorry to be out of the loop for so long. I bought a new computer and my old email
system was so out of date that I couldn't transfer my email addresses to my new
computer. Suffice it to say, typing in all of my mailing list didn't come to the top of my
to do list! Had a couple of messages today from Sandy Clifton that I thought were worth
passing on, so finally bit the bullet and worked on my list. While doing it, found out that
some people who I thought were on my old list weren't - my apologies to those of you
who are first hearing about this. Please let me know that you received this and make
other suggestions as who should be included on my new (and hopefully improved) list.
Anyway, here's the latest on the Physarum genome project. Regards, Jonatha
Begin forwarded message:
From: Sandra Clifton <sclifton@watson.wustl.edu>
Date: November 1, 2006 3:25:49 PM EST
To: Jonatha Gott <jmg13@case.edu>
Subject: Re: Physarum Genome
Hi Jonatha,
I will keep you posted. It just takes time to get things through each queue! Once we
have an initial assembly, the data will be posted for your group to take a quick look at
and determine that we have indeed sequenced Physarum (possibly for about a week), and
then the assembly will go public, upon approval. The data will then be available from
our ftp site for blasting and downloading, and it will be submitted to GenBank, as well.
Talk to you soon,
Sandy
Jonatha Gott wrote:
Thanks for the update, Sandy. I'll forward it to the Physarum community, as I'm sure
they'll be happy to hear things are finally progressing.
We do want to make sure that any libraries that you make are not lost. Please give us as
much lead time as possible on this - the Dicty group is willing to store our libraries, but I
haven't heard yet how their grant fared. We requested funding for freezers, etc. as they
probably won't have room for everything without additional freezer space.
Would also appreciate receiving updates periodically as to how things are going and
instructions as to how to access the data to pass on.
Thanks for getting back to me so quickly - Jonatha
On Nov 1, 2006, at 12:41 PM, Sandra Clifton wrote:
Begin forwarded message:
From: Sandra Clifton <sclifton@watson.wustl.edu>
Date: November 1, 2006 12:41:14 PM EST
To: Jonatha Gott <jmg13@case.edu>
Subject: Re: Physarum Genome
Hi Jonatha,
We are preparing to send the library through production. We still have not had a goahead on the project plan, but we are sure that it will be okay to go ahead and begin
sequencing. The original plan was to perform a 4X WGS with plasmid (3.7X) and
fosmid end sequences (0.3X). This will be assembled using the available EST sequences
from the community to assemble the data. We will evaluate the genome, and return at a
later date with a specific plan, armed with additional data. We want to see what the
genomic landscape looks like before going full bore for a 6-8X coverage. If it appears
that there is a preponderence of repeat DNA, we would like to consider 1) doing a Cot
curve and sampling the high Cot fraction to produce a Physarum-specific repeat database,
2) sequencing the low cot fraction to determine the unique regions, 3) preparing
fosmid filters for hybridization to identify and sequence clones of interest to the
community, 4) performing cDNA sequencing on the 454 Genome 20 Sequencer,
obtaining as much full length sequence as possible. Of course, these are just a series of
options that we might suggest, depending on what the original 4X tells us. I have a
feeling that this will be a "tricky" genome, and we will probably have to be creative in
our approaches.
We probably will not be doing an assembly until we have the initial 4X complement of
plamid and fosmid reads. However, all the reads will be submitted to the Trace Archive
in GenBank, and anyone can download them and do an assembly on their own. We
simply have so many organisms to assemble, that the disks are always full, and we have
to queue for assembly.
-Sandra W. Clifton, Ph.D.
Assistant Director Genome Sequencing Center
Campus Box 8501
4444 Forest Park Blvd
St Louis MO 63108
w 314-286-1467
f 314-286-1810
<sclifton@watson.wustl.edu>
Dr. Jonatha M. Gott, Associate Professor
Center for RNA Molecular Biology
Case Western Reserve University
10900 Euclid Avenue
Cleveland, OH 44106
phone: 216-368-3930
fax: 216-368-2010
email: jmg13@case.edu
website: http://www.rnaresearch.org
FedEx delivery address:
2109 Adelbert Road
CWRU - SOM Wood W113
Cleveland, OH 44106