Phage annotation pipeline taking advantage of protein structure comparison
We developed a workflow called Gut Phage genome annotation note (GPnote) for phage genome annotation. GPnote is an automated de novo genome annotation pipeline that integrates both the sequence-based and structure-based predictions of gene functions.
we employed VIGA (Gonzalez-Tortuero et al., 2018) as our annotation start point(which provides the BLAST Hit of RefSeqViral and VOGs/pVOGs Hit by profile HMM search) and further incorprated the HMM profile comparison Hits in PHROGs via hhsuite.Also we did hmmsearch against PFam database for more function indications. Besides all these sequence-based strategies, we achieved advanced structure-based annotation by ESM-Fold (Lin Zeming et al., 2023) structure prediction and FoldSeek (Michel van Kempen et al., 2023) 3Di structure search against the AFUniProt50 database.