[ensembl-dev] A question about genome annotation project

[Bronwen Aken]

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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