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gbouras13 / phold

Phage Annotation using Protein Structures
MIT License
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Inquiry on protein annotation #54

Open songmj86 opened 2 months ago

songmj86 commented 2 months ago

Description

Hi. I I am trying to annotate viral proteins

I do not have input format (genbank file) as the output generated from Pharokka resulted from the command "pharokka_proteins.py "

Is there any way to use Pharokka output obatined from "pharokka_proteins.py " as input for phold ?

Thanks !

gbouras13 commented 2 months ago

Hi @songmj86 ,

Yes. You can use these 2 commands

phold proteins-predict and phold proteins-compare.

This will be equivalent to running phold predict and phold compare on a genbank/nucleotideFASTA file

George

songmj86 commented 2 months ago

Thanks !

songmj86 commented 2 months ago

I missed another question

I used the protein fasta files as inputs to run Pharokka

Identical protein fasta files are not suitible formats for the input to run Phold ?? Then, do I need to use nucleotide sequences for CDS for input to run Phold predict & compare ?

Thanks!

gbouras13 commented 1 month ago

Hi @songmj86 ,

I am not sure what you mean but this question. Phold will accept amino acid FASTA (aka .faa) files using phold proteins-predict and proteins-compare.

George