[Arthropod] Arthropod genomes in progress?

Mark Blaxter via arthropod%40net.bio.net (by mark.blaxter from ed.ac.uk)
Wed Dec 9 16:28:48 EST 2009


Hi Terence
thanks for the info

A couple of comments and questions

- I have submitted many EST datasets in the past (standard Sanger  
ones) and havent been 'required' by NCBI dbEST to 'register' the  
'genome project' they derive from. Is this a new rule, or is it an  
aspiration?

- We have Illumina, Roche and AB instruments, and our user base is  
requesting 'whole' transcriptome and genome data generation ever more  
frequently, so it will be good to get a registry going. However,  
waiting till the data are submitted to GenBank/EMBL/DDBJ may not be  
what the community needs - I think I'd like to have a registry of  
genomes-in-progress and genomes-in-aspiration, so we can collaborate  
in data generation (someone might be doing a genome for the  
transcriptome I am generating, etc), data analysis (someone might be  
interested in the clade my genome is from) and thus copublication/web  
presentation. Is that what you meant Don?

- a question... the 'big' (or maybe thats 'vast' now!) genome centres  
are part of a global collaborative, and thus have their genomes-in- 
progress and genomes-in-waiting fasttracked to NCBI and other www  
sites. Ive tried to contact them via http://www.intlgenome.org/ but  
had no reply. Now that we are able to generate >10 Gbase/week of raw  
data in our centre alone, it would be good to open the club a little,  
no?

Mark

On 9 Dec 2009, at 20:22, Murphy, Terence (NIH/NLM/NCBI) [C] wrote:

> I second the motion to try and accumulate a more complete list of
> genomes in progress. Don referred to a partial table at NCBI:
> http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi
>
> This table is generated from the Genome Projects database
> (http://www.ncbi.nlm.nih.gov/genomeprj), which contains records
> describing various types of ongoing or finished genome projects. When
> whole genome, transcriptome, and other types of genome sequencing
> projects are submitted to GenBank, EMBL, or DDBJ, the submitter is
> required to also register their project in the Genome Projects  
> database.
> Thus, the Genome Projects database should have a complete listing  
> of all
> arthropod genomes with sequence in the public databases.
>
> Curators at NCBI used to create genome project records when projects
> were first started based on information from NHGRI or other sources.
> Now, in the age of cheap sequencing, we no longer have knowledge of  
> what
> projects are underway or the time to create projects proactively,  
> so the
> table of "in progress" genomes is a poor representation of what is
> currently underway.
>
> One option would be for those of you with projects that are nearing
> completion to go ahead and register your project at NCBI:
> http://www.ncbi.nlm.nih.gov/genomes/mpfsubmission.cgi
>
> This will give you a genome project ID that you will be needing for  
> your
> submission anyway, and your genome should appear on the "in progress"
> table above in a few days.
>
> I've heard of a lot of projects that are in the works, but I'm sure
> there are more coming and it would be useful to have a more complete
> listing of what to expect. These are exciting times!
>
> Let me know if you have any questions about the Genome Projects
> database, or anything else for that matter, and I'd be glad to help.
>
> Sincerely,
>
> -Terence
>
> -----
> Terence Murphy, Ph.D.
> RefSeq Project, Arthropod Genome Champion
> NCBI/NLM/NIH/DHHS
> 45 Center Drive, Room 4AS.37D-82
> Bethesda, MD  20892-6510
> Phone: 00-1-301-402-0990
> e-mail: murphyte from ncbi.nlm.nih.gov
>
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Professor Mark Blaxter
mark.blaxter from ed.ac.uk
http://www.nematodes.org/

Institute of Evolutionary Biology
University of Edinburgh
EH9 3JT




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