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tseemann / prokka

:zap: :aquarius: Rapid prokaryotic genome annotation
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How to annotate with custom database alone? #645

Open dineshkumarsrk opened 1 year ago

dineshkumarsrk commented 1 year ago

I need to annotate TAL effectors which is highly repetitive in nature. Therefore, I would like to create TAL effector database with the available TALE protein sequences. Therefore, I would like to use TAL effector database alone without using other default db installed in the prokka pipeline. In detail I would like to have TALEs annotation only for my genome of interest. Could you please help me to do the same.

Thank you in advance.

abhijeetsingh1704 commented 1 year ago

Since the genome doesn't only have TAL effectors, it would not make sense to use only that database to annotate the genome. But you can still use TAL effector database as a reference fasta file and use annotate with reference "--proteins" version in prokka. The other way which you want to do can be done with blast/diamond or similar.