interpro/interproscan repository overview

⁠Quick reference

• Maintained by:
  InterPro⁠

• Where to get help:
  InterProScan 5 documentation⁠, helpdesk support⁠

⁠What is InterProScan 5?

InterPro is a database which integrates together predictive information about proteins’ function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains.

Users who have novel nucleotide or protein sequences that they wish to functionally characterise can use the software package InterProScan to run the scanning algorithms from the InterPro database in an integrated way. Sequences are submitted in FASTA format. Matches are then calculated against all of the required member database’s signatures and the results are then output in a variety of formats.

⁠How to use this image

⁠Get InterProScan 5 data

This image does not include data required to run InterProScan 5, which need to be downloaded separately. For the latest InterProScan 5 release (5.78-109.0), data can be downloaded with the following command:

curl -O http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.78-109.0/alt/interproscan-data-5.78-109.0.tar.gz

We always recommend verifying your downloads for corruption:

curl -O http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.78-109.0/alt/interproscan-data-5.78-109.0.tar.gz.md5
md5sum -c interproscan-data-5.78-109.0.tar.gz.md5

Finally, extract data files from the downloaded archive:

tar -pxzf interproscan-data-5.78-109.0.tar.gz

The data will be extracted to interproscan-5.78-109.0/data.

⁠Example

Download a sequence:

curl -O https://rest.uniprot.org/uniprotkb/A0A125YHZ8.fasta

Run the image to scan the sequence:

docker run \
    --rm \
    -w $PWD \
    -v $PWD:$PWD \
    -v $PWD/interproscan-5.78-109.0/data:/opt/interproscan/data \
    interpro/interproscan:5.78-109.0 \
    --input A0A125YHZ8.fasta

⁠Phobius, SignalP, TMHMM

While InterProScan 5 supports Phobius 1.01, SignalP 4.1, and TMHMM 2.0, the analyses are disabled as they contain licensed components.

In order to activate them, please obtain the relevant license and files from the providers:

• Phobius: Download⁠
• SignalP: Download⁠
• TMHMM: Download⁠

Like the InterProScan 5 Docker image expects the data files to be available in /opt/interproscan/data, it expects the licensed components to be available in /opt/interproscan/licensed. Once you have obtained the licensed components, place them in a licensed directory that follows the same structure:

licensed/
├── phobius
│   ├── decodeanhmm
│   ├── phobius.model
│   ├── phobius.options
│   └── phobius.pl
├── signalp
│   ├── bin
│   ├── lib
│   ├── signalp
│   └── syn
└── tmhmm
    ├── decodeanhmm.Linux_x86_64
    └── TMHMM2.0.model

Important: the SignalP Perl script at licensed/signalp/signalp must be edited. Make sure to change the full path to the SignalP directory so it is found from the container:

BEGIN {
    $ENV{SIGNALP} = '/opt/interproscan/licensed/signalp';
}

Then run InterProScan 5 with the additional bind mount (-v $PWD/licensed:/opt/interproscan/licensed):

docker run \
    --rm \
    -w $PWD \
    -v $PWD:$PWD \
    -v $PWD/interproscan-5.78-109.0/data:/opt/interproscan/data \
    -v $PWD/licensed:/opt/interproscan/licensed \
    interpro/interproscan:5.78-109.0 \
    --input A0A125YHZ8.fasta