I have 10 transcripts where I need to do 5 peptide sequence alignments (2 transcripts per alignment). I need to do this in order to indicate which amino acids lead to which domains.
My questions are two:
Is there a tool I can use from my laptop that aligns peptide sequences? Because results from the clustal omega peptide alignments web service only last two weeks, they're not ideal for replicability in a paper.
The ultimate aim is to use those alignments and domain classifications to a project I am writing and I am trying to make it as presentable and scientific as possible. Any suggestions on how to make peptide alignments and annotations on peptide alignments (which indicate protein domains) look presentable for a paper or if a paper has already shown peptide alignments in a presentable way that would be highly appreciated.