Final answer:
Genome annotation is the process that generates an auto-annotation of a phage genome, performs protein searches, and stores the evidence for easy review in a gene-by-gene manner.
Step-by-step explanation:
The process that generates an auto-annotation of a phage genome, automatically performs protein searches using BLASTP and HHPred, and stores the evidence in a gene-by-gene manner is called genome annotation. Genome annotation is the process of attaching biological information to gene sequences. It helps in assigning functions to proteins encoded by specific sequences. The evidence obtained from protein searches using BLASTP and HHPred is stored in a way that facilitates easy review of the information on a gene-by-gene basis.