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<font face="Helvetica, Arial, sans-serif">Hi Ana,<br>
<br>
I've forwarded your questions to the nGASP group so they can answer
your questions directly.<br>
<br>
best regards,<br>
<br>
John<br>
<br>
<br>
</font><br>
Ana Rodrigues wrote:
<blockquote
cite="mid:acf4936a0803141635o250b5184xda9c7ebf58bee0fe@mail.gmail.com"
type="cite">
<pre wrap="">Dear Dr. Spieth,
Just a quick follow-up email to let you know that I am making
extensive use of the brenneri preliminary assembly.
I am working on establishing Caernorhabditis orthology and paralogy
sets that cover C. elegans extensively, so that I can use this rich
comparative information for validating transcription factor binding
sites.
To add brenneri to our previous (3 worm) system, we performed gene
predictions based on elegans homology (with genewise). These are
reasonable for our purposes, but we are keen to use the nGASP
predictions - is there any further development on when these will be
released?
Are there any plans to publish comparative analysis of the 4/5 worms?
We are now delving deeper into the details of the ortholog and paralog
sets, and finding them interesting in themselves. There is lots of
scope for improving the sets and many interesting examples of species
specific expansions, etc. Is this something that would be of interest
to the annotation group?
Many thanks,
Ana
On Thu, Jan 10, 2008 at 10:21 AM, John Spieth <a class="moz-txt-link-rfc2396E" href="mailto:jspieth@watson.wustl.edu"><jspieth@watson.wustl.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap=""> Hi Ana,
Happy New Year to you too, Ana.
No, there are not any gff files for the brenneri genome yet., but I'm happy
to hear there are people interested in using this genome. There is a
preliminary assembly based on WGS coverage of ~9x currently available at
GenBank (accession ABEG01000000) and on the WormBase ftp site
(<a class="moz-txt-link-freetext" href="ftp://ftp.wormbase.org/pub/wormbase/genomes/brenneri/2007.01-draft_assembly">ftp://ftp.wormbase.org/pub/wormbase/genomes/brenneri/2007.01-draft_assembly</a>).
The nGASP project (<a class="moz-txt-link-freetext" href="http://www.wormbase.org/wiki/index.php/NGASP">http://www.wormbase.org/wiki/index.php/NGASP</a>) is now
calling a brenneri gene set based on the preliminary assembly, which will
then be displayed on a Genome Browser and gff files available from WormBase.
When these are available there will be an announcement on the WormBase
homepage (<a class="moz-txt-link-freetext" href="http://wormbase.org/">http://wormbase.org/</a>). Hopefully this will come about in the next
month or so. Also, please feel free to drop me email anytime asking about
the status of brenneri.
cheers,
John
<a class="moz-txt-link-abbreviated" href="mailto:arodrigues@salk.edu">arodrigues@salk.edu</a> wrote:
To: John Spieth
From: Ana Rodrigues
Email: <a class="moz-txt-link-abbreviated" href="mailto:arodrigues@salk.edu">arodrigues@salk.edu</a>
Subject: C. brenneri gff
Comments: Are there any preliminary gff files for the C. brenneri genome,
that my web hunting has missed?
Thanks for you help and Happy New Year,
Ana
</pre>
</blockquote>
<pre wrap=""><!---->
</pre>
</blockquote>
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