InterproScan

Protein domain annotation by searching sequences against integrated signature databases from InterPro.

Annotation codeGitHub languageDocs menu_bookPaper scheduleApril 3, 2026

Installation

Create a folder for your program:

mkdir my_interproscan
cd my_interproscan

Get the required files:

wget https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.76-107.0/interproscan-5.76-107.0-64-bit.tar.gz
wget https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.76-107.0/interproscan-5.76-107.0-64-bit.tar.gz.md5

Check if the download was successful

md5sum -c interproscan-5.76-107.0-64-bit.tar.gz.md5

info

If successful, it should show: interproscan-5.75-106.0-64-bit.tar.gz: OK

Extract the file

tar -pxvzf interproscan-5.76-107.0-64-bit.tar.gz

Go to the folder where the files were extracted:

cd interproscan-5.76-107.0

Before you run InterProScan for the first time, run the following command to prepare the HMM profiles used by InterPro:

python3 setup.py -f interproscan.properties

Import InterProScan location to the PATH

To be able to run InterProScan from any directory, run this before each session. Make sure to put the location where your InterProScan is installed:

export PATH="/home/interproscan-5.76-107.0:/$PATH"

Alternative Installation

You can also use conda to install InterProScan:

conda install bioconda::interproscan

Run

interproscan.sh -i genomeA.faa -cpu 30

The Headers of Your Output

Scaffold_position	MD5_difest	Length	DB	Database_Signature	Description	Start		Stop		e-value	Status	Date	InterPro_annotation	Interpro_description

Column	Description
Scaffold_position	Identifier of the query sequence
MD5_difest	MD5 digest of the query sequence
Length	Length of the query sequence
DB	Member database that generated the match
Database_Signature	Accession of the matched database entry
Description	Description of the matched database entry
Start / Stop	Start and stop positions of the match on the query sequence
e-value	E-value of the match
Status	Status of the match (T = true positive)
Date	Date the analysis was run
InterPro_annotation	InterPro accession for the integrated entry
Interpro_description	Description of the InterPro integrated entry