I agree with this answer. You only got the structural annotation (ORF coordinates) from BRAKER. Using an ortholog finder to assign a protein/gene ID is possible, but only if you use the same species as source and target (genomes to find orthologs) and those IDs have been validated.
BRAKER3 genome annotation
i wanted to annotate a genome file available In NCBI. I used RNAseq data available for the same organism In EBISRA and a set of proteins available in NCBI as input to BRAKER3 as evidence. I got the BRAKER 3 result as a GFF3 file. it gave the mRNA positions in the genome but did not give the name or id of proteins or mRNA. how should I annotate further ????
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[BRAKER3] gave the mRNA positions in the genome but did not give the name or id of proteins or mRNA
I guess you want to know which proteins in the newly annotated genome correspond to proteins in the reference annotation(s). One option is to run a program for finding orthologs, e.g. orthofinder, but I'd like to hear of alternatives.
EDIT:
Consider also liftoff: "accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species"
Possibly related: You can also annotate proteins with pfam domains using for example hmmer. This is biologically more meaningful than assigning names from one assembly to another.
If any useful I have a snakemake pipeline for running braker, galba, merge annotations from these two, and annotate with pfam.
I also have this exact same question. I have my entire genome annotated and a braker.GTF file, but without protein "product" names.
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I suggest searching for the difference between structural annotation (identifying the coordinates of the ORFs in a sequence) and functional annotation (assigning a function or the most likely function to an ORF/protein). Those are independent processes. As far as I remember, BRAKER doesn't include the functional annotation, that's why you can't find any "product names".
Perhaps worth keeping in mind that protein "product" names is only a human construct. At the biological level you have protein biochemical properties and phylogenetic relationships. So while it's useful to assign protein names according to a reference annotation, ultimately you are still looking for orthologs.
Yes, but functional annotation permits one to compare conservation of function between taxa; which is helpful.
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Could you share some lines from your gff3?
ya sure
Perhaps eggNOG-MAPPER can be useful for functional annotation:
This will give you the description of your proteins.