Splice model

[arunvv90]

Hi,
Thank you for the great tool!! I am using it for virus annotation(Ictalurid herpesvirus). Testing went very well. In the last update, two splice models are added. In the earlier version, I was using the default version. I was wondering which model would be appropriate for my case(I guess the general model?). Another question is about the GFF format. My GFF looks like this

C02-169_draft1	miniprot	mRNA	33598	35094	2600	+	.	ID=C02-169_ORF25_000001;Identity=0.9940;Positive=0.9960;Target=C02-169_ORF25 1 498

Can you please tell me what is 2600, Identity(nucleotide identity or amino acid identity), Positive=0.9960, and the last two columns(1,498)? Please forgive me for these silly questions from a newcomer. There are not many good tools out there for virus annotation and most of them fail with introns like herpesvirus. Your tool seems very promising.

[lh3]

I don't know what splice site look like in Ictalurid herpesvirus (is it GT-AG?). It is safer to use -j1, which is now the default and is equivalent to the splice model in v0.4.

nucleotide identity or amino acid identity

Amino acid. miniprot doesn't see the nucleotide sequences of query genes.

the last two columns

See the GFF3 spec. It is the region of the query protein aligned

[arunvv90]

Thank you for the quick reply. Splice junctions in the virus are major GT-AG or minor AT-AC

[lh3]

Thanks. I didn't know that. Miniprot considers GT-AG, GC-AG and AT-AC. I think it should work.

PS: also forgot to answer – 2600 is the alignment score without considering introns.