Novel protein identification

Question

[a.mostafa5050]

Hi everybody,

I am doing a functional metagenomic study. I did the annotation of protein sequences using HMMER against the Resfam database.

The question is how can I know that one of the predicted AR protein is a NOVEL??

Thanks

Answer 1

[Qiongyi]

A general guide is: If you find a predicted protein which is not previously documented (e.g. not listed in the GTF/GFF), we think this protein is novel (of course after validation).

[a.mostafa5050]

Do you mean searching in different databases such as NCBI and Uniprot to search for the function of the predicted protein??

[Qiongyi]

Yes. If you don't have a genome & GTF/GFF to check, blastp to known protein databases sounds OK. Given that you can validate this protein, if it is not a known protein, it is novel.

[a.mostafa5050]

Thanks a bundle, :) :)