search

tomdeman-bio / HMMer-scripts-

Scripts that deal with HMMer output
0 stars 1 forks source link

HMMER protein annotation #1

Open Ahmedbargheet opened 3 years ago

Ahmedbargheet commented 3 years ago

Hi everybody,

I am doing a functional metagenomic study. I did the annotation of protein sequences using HMMER against the Resfam database. I mean I have a list of predicted resistance genes from the Resfam database which is responsible for antimicrobial resistance. Therefore, in my data, I have some genes that confer the resistance. How can I know if my data has a novel gene which responsible for antimicrobial resistance?

Thanks

tomdeman-bio commented 3 years ago

The scripts that I provided aid in estimating which proteins are more or less likely to be real (protein sequences that lack a functional domain or motif are less likely to be real). If you want to discover novel AR proteins I would suggest identifying proteins with full domains that are related to AMR (e.g. PFAM domain PF00144) and then see if those are already known or not.

Good luck

Op za 5 dec. 2020 om 15:08 schreef Ahmedbargheet notifications@github.com:

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

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/tomdeman-bio/HMMer-scripts-/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABIDXZHZWIBNEYOPSLATE3DSTKHMZANCNFSM4UOY235Q .