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Reaching organisms that have whole genome annotation through perl

Does someone know if there is a way to retrieve the species name / taxid of organisms that have whole genome annotation ? I would like to be able to do that in perl. My first thought was to look at NCBI through a Bioperl method...but I didn't find.

Any help is appreciated.

genome
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written by Juke34 Juke34

Could you be more specifically what you mean with whole genome annotation? The human genome is probably one of the best studied and annotated genome, but I wouldn't claim that the whole genome is annotated.

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written by WouterDeCoster WouterDeCoster

Yes sure, I will try to be more precise. By whole genome annotation I mean a whole genome assembly where an annotation exists. I consider a genome assembly or a genome annotation as "whole/complete" if an effort in that sens has been done. I don't take into account if the annotation is good or bad, if some genes are missing or if the assembly is 80-90-99% complete.

Btw, I don't know yet any people ready to claim that a genome is really "complete" at the assembly and the annotation level... even for the human one.

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written by Juke34 Juke34

Yes thank you. It could be a solution. Even if I wanted to avoid to use the Ensembl API I think it's a solution. But I'm still not convince... the INSDC databases as NCBI are complete but I doubt about Ensembl. I guess Ensembl contains a sub-part of whole genomes...

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written by Juke34 Juke34

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