Interpretation of results

[Handymanalan]

Hi deprekate,

I have used Phanotate but I am not sure what the output means. I ran it through a single metagenomics-assembled genome (MAG), and got multiple start and stoping codon frames in one single contigs.

The scores are all negative and are those E-values? I am not sure which contig to choose.
After that should is the best way to identify phages Blasting the sequences?

I am new in extracting phage sequences from metagenomics so any advice is greatly appreciated.

Cheers and many thanks

Alan

[deprekate]

Hi, sorry for lag, I never got notifications on this thread. I am not sure what you mean when you say you get multiple start and stopping codon frames. You should get multiple gene calls for every contig (provided they are long enough, and thus have multiple genes).
If the gene calls overlap, that is normal, since phage genomes are very compressed, and most of their gene ends overlap each other.
The scores are just rough quasi-probabilty scores. They were added as a way to filter out low scoring ORFs, poor scoring calls will be large and positive.
You can mostly take all the calls are returned.