annotation merge

[Shlomo Blum]

Hi,

I would like to compare the annotation of a bacterial draft genome made by two different pipelines (PGAAP and RAST).

Any ideas how to do that?

Is it possible to "merge" the annotations into a single file? Say, a genbank file?

Thanks

[Wallysb01]

Check out maker2 for merging them. Comparing them would be Eval.

[Shlomo Blum]

Do these tools work with prokaryote genomes?

Actually, I would like to compare gene by gene annotation from each source and not only to compare overall quality.

While PGAAP output comes ready for submission for NCBI, the RAST output assigns genes into subsystems. That's why I would like to work with both outputs, but it would be nice to "join" the whole information together and also to correct errors that might exist in one or the other.

[Wallysb01]

Maker2 does work with prokaryote genomes.

And for gene by gene annotation comparison I don't know of anything and that sounds like a very difficult task. I think the best way would really be to just visualize them in a genome viewer.