Input Sequences

Open Kudzai-H opened this issue 7 months ago • 1 comments

Hi,

I would like to use AMPlify to predict AMPs in transcriptomes from a starfish. However, I noticed that the input sequences in the example workflow were proteins. Do my sequences also have to be proteins? Or can Amplify take nucleotide sequences?

Thank you, Kudzai

Jun 18 '25 18:06 Kudzai-H

Hi @Kudzai-H,

Thanks for contacting us regarding your questions. Yes, the AMPlify inputs have to be protein sequences.

We have developed an AMP discovery pipeline (https://github.com/bcgsc/rAMPage) which takes RNA-seq reads as the input, which may be related to what you are doing. The rAMPage pipeline uses AMPlify as its discovery engine.

Please feel free to let us know if you have further questions.

Thanks! Chenkai

Jun 28 '25 22:06 mark0428