start and end position coordinates in csv input file

[Former user]

Hi Jean

I am writing out my own csv file for import into Peptigram. I noticed in your example csv and information on your web page that the Start and End Position is relative to the Signal peptide of a protein (i.e. its removed). Unfortunately we do not have this information at hand so I am writing out the original start and end co-ordinates of the peptides based on the Uniprot sequence (precursor). Is this OK?

Thanks - nice tool for the community.

Best Eugene

[Jean Manguy]

I'm going to check, but if I remember the default is to work with the basic coordinates mapping to uniprot sequence, the signal peptide "correction" is just a hack to allow peptides mapped from the mature protein (length of the signal peptide taken from uniprot, if the sequence of the "corrected" peptide doesn't match the sequence of the peptide: there is no correction)