Hi all,

. I locally run InterProScan (interproscan-5.14-53.0) for finding the protein domain on translated de novo assembled transcriptome. I used the following command:

./interproscan.sh -i file1.pep -t p -o file1_intro.xml -f xml -appl Pfam, ProDom, ProSiteProfiles -goterms -iprlookup

It generated a 60 MB file, but I don't know how to extract the required information from this output. It was my first experience and I have no idea how to handle the results. Could you please let me know if I should sort or filter the output based on something like e-value, similar to blast. If your response is positive, please kindly tell me how I can do it? Also, I want to know which protein domains/families existed in my query file and what are their frequencies?

Thanks