Hi Robyn, I see no one has answered your question, so I'll try and help although I don't have experience with protter.
It think you've misunderstood TPP a little. It's a pipeline for analyzing protein mass spectrometry data. Thus you need both a fasta file of sequences and mass spectrometry data as inputs. Protter can then apparently take the output and show where on your protein sequence you find the peptides that you identified in your mass spectrometry data. So you can't use InterPro results files as an input to the TPP. If you want to produce nice diagrams of protein sequences with the domains identifed by interpro scan there are some other options (besides those diagrams you get from the web version of interpro). For example IBs (http://ibs.biocuckoo.org/) is a GUI based desktop program where you can manually input the domain boundaries or other features of interest. Personally I make all such diagrams in R using my own code. However there are various options out there (https://omictools.com/protein-visualization-category) depending on exactly what you want to do and what sort of data you want to display. There might be ways to get the information you require into protter, but as I said I have no experience of using it. Hope this helps a little, Alastair Am Mittwoch, 5. September 2018 17:33:22 UTC+2 schrieb Robyn Leigh Smith: > > Hi all > > Please, would someone assist me? I am using the proteome of a large > non-model organism to look at a set of novel proteins. I have a .fasta file > of there primary structure and the domains inferred by InterPro. The > results generated by InterPro are in a .xml file, but I cannot import it > into Protter. What is the difference between the file generated by InterPro > and that generated by TPP? I am battling to get the TPP pipeline to run > because my proteins are novel so are not stored on any of the databases, > and it seemingly needs more information than the amino acid sequence. > > PLEASE HELP! > > Thank you in advance > > Kind Regards > Robyn > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
