From jspieth at watson.wustl.edu  Sat Mar 15 00:06:25 2008
From: jspieth at watson.wustl.edu (John Spieth)
Date: Fri, 14 Mar 2008 23:06:25 -0500
Subject: [Ngasp-help] Re: C. brenneri gff
In-Reply-To: <acf4936a0803141635o250b5184xda9c7ebf58bee0fe@mail.gmail.com>
References: <20080110001513.DF993150197@linuscs19.gsc.wustl.edu>	
	<47865422.3030802@watson.wustl.edu>
	<acf4936a0803141635o250b5184xda9c7ebf58bee0fe@mail.gmail.com>
Message-ID: <47DB4B41.9080709@watson.wustl.edu>

Hi Ana,

I've forwarded your questions to the nGASP group so they can answer your 
questions directly.

best regards,

John



Ana Rodrigues wrote:
> 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 <jspieth at watson.wustl.edu> wrote:
>   
>>  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
>> (ftp://ftp.wormbase.org/pub/wormbase/genomes/brenneri/2007.01-draft_assembly).
>> The nGASP project (http://www.wormbase.org/wiki/index.php/NGASP) 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 (http://wormbase.org/).  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
>>
>>
>>  arodrigues at salk.edu wrote:
>>  To: John Spieth
>>  From: Ana Rodrigues
>>  Email: arodrigues at salk.edu
>>  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
>>
>>
>>
>>     
>
>
>
>   
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