[ensembl-dev] Genome coverage

[Daniel Lawson]

Dear Sam,

You should look at measures of completeness in the assembly based on
conserved 1:1 orthologs across species.

Older small scale set CEGMA (Korf lab,
http://bioinformatics.oxfordjournals.org/content/23/9/1061.full#sec-2)
Latest large scale BUSCO (Waterhouse NAR 2012 OrthoDB paper
http://nar.oxfordjournals.org/content/41/D1/D358.long)

regards
Dan



On 11 September 2013 15:21, Sam Seaver <samseaver at gmail.com> wrote:

> Dear Ensembl,
>
> It's recently come to my somewhat naive attention that many eukaryotic
> genomes are not fully sequenced. In other words, for the list of genes that
> I download for any species, I should expect that there is a fraction of
> genes missing.  What I'm trying to discover is whether I can reliably find
> an estimate of this for each of the plant species I'm exploring.
>
> I suspect that I would have to go back to each of the papers describing
> the original genome, to see if the authors give an estimate.  Indeed, I
> understand that this estimate is probably based on a comparative analysis
> with other genomes.  Regardless, I'm hoping that somewhere within Ensembl,
> there is a set of statistics that I can use directly, to declare how
> "complete" a genome is for any given plant.  Does this exist?
>
> Thanks
> Sam Seaver
>
> --
> Postdoctoral Fellow
> Mathematics and Computer Science Division
> Argonne National Laboratory
> 9700 S. Cass Avenue
> Argonne, IL 60439
>
> http://www.linkedin.com/pub/sam-seaver/0/412/168
> samseaver at gmail.com
> (773) 796-7144
>
> "We shall not cease from exploration
> And the end of all our exploring
> Will be to arrive where we started
> And know the place for the first time."
>    --T. S. Eliot
>
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-- 
Ensembl Genomes | VectorBase | i5K insect genome initiative
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