I am trying to annotate genes for a phage genome (Salmonella phagevB SPuM_SP116; Accession: KP010413.1) obtained from a blast hit of an assembled contig. Could you please tell me the best way to do it?
I tried DNAmaster but, for some reason it doesn't give me ORF/CDS (predicted by Glimmer/GeneMark - softwares integrated in DNAmaster) and only gives me tRNAs (predicted by Aragorn - software integrated in DNAmaster); may be I am doing something wrong. Whereas, when I run Glimmer locally, it gives me ORFs. I would really appreciate your input on what you think could be wrong here?
And, I am trying to download fasta file of the phage "Salmonella phagevB SPuM_SP116" from the https://phagesdb.org/phages/ website but I do not find this phage there. Can you please let me know if am missing something here?
Thank you very much! DK