Incorrect virus names in U-RVDBv12.2-prot.fasta

[terrycojones]

Hi. First of all, thanks so much for all this work, it looks like a very promising middle ground between the small selection of the refseq database and the unruly enormous nt database.

I have found a couple of cases of what should be virus names (in [...] at the end of the sequence ids) that are actually species names.

$ grep -F '[Gorilla gorilla]' U-RVDBv12.2-prot.fasta
>acc|GENBANK|CAE12263.1|GENBANK|AJ577596|FRD envelope protein [Gorilla gorilla]
>acc|GENBANK|AAM68167.1|GENBANK|AY101588|envelope glycoprotein [Gorilla gorilla]
>acc|GENBANK|AAM68168.1|GENBANK|AY101589|envelope glycoprotein [Gorilla gorilla]
>acc|GENBANK|ABB73024.1|GENBANK|DQ256474|syncytin 1 [Gorilla gorilla]
>acc|GENBANK|AGI61266.1|GENBANK|KC010498|envelope protein ENVV1 [Gorilla gorilla]
>acc|GENBANK|AGI61275.1|GENBANK|KC010510|envelope protein ENVV2 [Gorilla gorilla]

and the same occurs for a grep on [Homo sapiens], though with many more hits:

$ grep -F '[Homo sapiens]' U-RVDBv12.2-prot.fasta | head -n 10
>acc|GENBANK|BAB47555.1|GENBANK|AB050996|envelope protein [Homo sapiens]
>acc|GENBANK|BAB47556.1|GENBANK|AB050999|envelope protein [Homo sapiens]
>acc|GENBANK|BAB47557.1|GENBANK|AB051000|envelope protein [Homo sapiens]
>acc|GENBANK|BAB47558.1|GENBANK|AB051004|envelope protein [Homo sapiens]
>acc|GENBANK|BAB47559.1|GENBANK|AB051007|envelope protein [Homo sapiens]
>acc|GENBANK|BAB47560.1|GENBANK|AB051008|envelope protein [Homo sapiens]
>acc|GENBANK|BAB47561.1|GENBANK|AB051009|envelope protein [Homo sapiens]
>acc|GENBANK|BAB47562.1|GENBANK|AB051010|envelope protein [Homo sapiens]
>acc|GENBANK|BAG06168.1|GENBANK|AB266802|putative retroviral envelope protein [Homo sapiens]
>acc|GENBANK|BAN04646.1|GENBANK|AB610407|suppressyn [Homo sapiens]

Regards, Terry

[terrycojones]

This seems to only be an issue with the protein version of RVDB. I'll ask them. Feel free to close this.

[terrycojones]

I've mailed Marc & Thomas about this. Closing.

[ArifaKhanLab]

They are endogenous (retro)virus (EN(R)V) sequences existing in their host's genome. We are working on the solutions to determine the sequences belong to host or EN(R)V for those particular cases.

[terrycojones]

Thanks @ArifaKhanLab !