[ensembl-dev] Is D. melangostar Ensembl DNA is the same as BDGP assembly release 5/dm3?

[Karyn Megy]

Hi Sergei, 

> In the D. melanogaster page it says
> (http://uswest.ensembl.org/Drosophila_melanogaster/Info/Index/):
> 
> "The genomic sequence is based on BDGP assembly release 5 (April 2006)".
> 
> I assume "based" mean that there changes in Ensembl DNA in Ensembl
> compare to BDGP R5/dm3 from Apr. 2006?

We don't change anything to the assembly, or to the set of genes, we just map additional features.
We will change the wording to make it clearer.

> In the drop-down menu, where "Previous assemblies" are, it is possible
> to choose BDGP5.25, BDGP5.13 etc. and if I click on "Download Fruitfly
> genome sequence" then I see that files have BDGP5.65 in their names.

Note that if you select another assembly/gene build, you need to click on "Go to archive" to be able to see data for this assembly.

The name "BDGP5.65"  means:   Berkley Drosophila Genome Project, '5' is the assembly, '65' is the Ensembl release, as you guessed.

The name should also have contained '25', for the genebuild  (see previous release: ftp://ftp.ensembl.org/pub/release-64/fasta/drosophila_melanogaster/dna/  -->  "Drosophila_melanogaster.BDGP5.25.63.dna.chromosome.2L.fa.gz") - we will fix this for the next release. It's just a naming issue, no data have changed. 

I hope it helps. Don't hesitate to contact us if you would like more details.

Best regards,
Karyn.


--
*************************************
              Karyn Megy, PhD
   VectorBase / EnsemblGenomes

European Bioinformatics Institute     
Wellcome Trust Genome Campus 
          Hinxton  CB10 1SD - UK 

Phone: +44.1223.49.25.92
*************************************



On 15 Feb 2012, at 08:33, Sergei Manakov wrote:

> Hello,
> 
> In the D. melanogaster page it says
> (http://uswest.ensembl.org/Drosophila_melanogaster/Info/Index/):
> 
> "The genomic sequence is based on BDGP assembly release 5 (April 2006)".
> 
> I assume "based" mean that there changes in Ensembl DNA in Ensembl
> compare to BDGP R5/dm3 from Apr. 2006?
> 
> In the drop-down menu, where "Previous assemblies" are, it is possible
> to choose BDGP5.25, BDGP5.13 etc. and if I click on "Download Fruitfly
> genome sequence" then I see that files have BDGP5.65 in their names.
> Does it mean that currently a D. melanogaster genome is of BDGP5.65
> assembly, or does it mean BDGP5 assembly, and 65 refers to the current
> ensembl release?
> 
> It would be very much appreciated if somebody could clarify this.
> 
> thanks,
> Sergei
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/