I have to know if in my protein there is a specific short motif (3aa), how many times it occurs and in which positions. Does anyone know if it exists any online tool that allow me to perform this analysis?
You can use geneious software, it is not free, but you can download the trial.
You can use ScanProsite:
http://prosite.expasy.org/scanprosite/
Select "Option 3 - Submit PROTEIN sequences and MOTIFS to scan them against each other."
https://www.expasy.org/proteomics
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