Protein Domain Comparison Of Interproscan Gff Files

Question

[alejandroriglesias]

Hi everyone:

First of all, I'm new to BioPerl, so I do not have a lot of knowledge on it. I have several GFF3 output files from various InterProscan analyses. The thing is I have to compare the GFF3 file of a given protein with the GFF3 file of another protein, to check if the protein domains of each protein are the same, and that should tell me if they are the same protein or not, let's say. I have looked in several pages to try and find a solution, but I can't come up with anything. Do you have any idea or suggestion for doing this?

Thank you very much in advance,

Alex.

[chevivien]

if i got you message well...i think you can perform interproscan analysis using the standalone version provided inhttps://code.google.com/p/interproscan/wiki/HowToDownload ,you will get a tsv file if you use default parameters.Then you can use python or perl script to extract the domains you are interested in...

[alejandroriglesias]

Ok, thanks a lot. I am running the interproscan using the standalone version, as you said. So gff3 files is not the best format to get the domains from, then?

Thanks again.

[chevivien]

i would rather use tsv format since it is easy to extract the domain using a script..

[Michael]

This is a good recommendation. By default, a TSV file is generated for protein sequences, so it is possibly in the output folder already. Also, if you want to compare only few proteins visually, the HTML output can be useful.