[ensembl-dev] A question about genome annotation project

[Zhang Di]

Thank you, Bronwen.

Actually I'm not only interested in learning the annotation system, but
have such an project at hand as well. As I mentioned before, I have been
trying to use the pipeline myself for a year. By now, I have done some
analyses, such as raw compute, Exonerate2genes, Similarity annotation, and
also have tried whole genome alignment projection. I'm not sure if I did
them in the best way, or even the right way as you guys would do. So now,
any advice?

And another two questions: May I just use my own annotation in a paper, or
it is better to wait for Ensembl to complete the analyses? If I want to
upload my genome to Ensembl, to whom should I contact?



On Tue, Jan 22, 2013 at 11:35 PM, Bronwen Aken <ba1 at sanger.ac.uk> wrote:

> Good afternoon,
>
> The assemblies that we annotate in Ensembl are always produced by other
> groups. After the external group has finished sequencing and assembly, the
> assemblies are deposited into the INSDC public database (ENA, NCBI, DDBJ)
> where we can download it. (Ensembl doesn't generate genome assemblies.)
>
> The Ensembl gene annotation team is responsible for downloading the genome
> assemblies, importing them into an Ensembl core database, and then running
> the annotation system eg. repeat-masking, cdna and protein alignments,
> RNAseq-based models, and finally the Ensembl gene set. Each person in the
> team will take one species for annotation, and do all the work from
> downloading the assembly to producing the final gene set. These are big
> projects; each genebuild takes on average 2 - 4 months. You're right, there
> are a lot of analyses - especially now that we are routinely using RNAseq
> data in our genebuilds.
>
> If you are interested in learning more about the Ensembl gene annotation
> system, please look out for our mini genebuild workshops. We usually hold
> one just before the Genome Informatics conference. These workshops
> introduce participants to the basics of the rulemanager and pipeline. Also,
> you could contact helpdesk at ensembl.org about our geek-for-a-week program.
>
> Kind regards,
> Bronwen
>
>
> On 16 Jan 2013, at 11:26, Zhang Di wrote:
>
> > Hi,
> >
> >    I have been trying to annotate a de novo sequenced genome with the
> ensembl pipeline for about a year. The more analyses I did, the more I was
> confused. They seemed too complicate to be done by one person.
> >    So, how are are these projects usually handled? Do the labs who
> sequenced the genome always annotate it themselves, or they can cooperate
> with the ensembl team, and ensembl annotate the genome?
> >
> > Reguards,
> >
> > --
> > Zhang Di _______________________________________________
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>
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-- 
Zhang Di
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