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5.0 years ago
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Recently I am working on comparative genomics , I usually used protein sequence database which come fromepredicted gene models. And I found out some species only have genome assemblies and usually their assembly quality is not very good. So why some genome assemblies don't have annotation?
Assuming the genome assembly authors have made annotations, and the genome assembly is submitted to NCBI, it is notoriously difficult to include annotations with an NCBI genome assembly submission (this is only recently changing with tools like GAG). Ultimately, most submissions just submit the genome assembly without annotations.
I thought NCBI was automatically annotating all submissions now anyway though?
Only if you submit to the prokaryotic genome annotation/eukaryotic genome annotation submission pipeline.
For Eukaryotic genomes you have to contact NCBI by using "Request Annotation" tab at the top of this page. That link takes you to a ticket submission page. Fill out the information and then someone from NCBI will get in touch.
I don't really know. It doesn't seem like they are or if they are it is only for the initial versions of genomes and not alternative assemblies.
Because annotating is hard.