Help - InterProScan FAQ

This FAQ aims to answer questions specific to the running of InterProScan from EMBL-EBI's website. For more general information about InterProScan please read the stand-alone InterProScan documentation (Readme file or FAQ).


Input questions

Results questions

Getting further help

What version of InterProScan is run at the EBI website?

For the precise version number of InterProScan being run please go to the submission details tab from your job results.

How do I reference use of InterProScan at the EBI website?

Please cite use of InterProScan with the following:

InterProScan - an integration platform for the signature-recognition methods in InterPro. Zdobnov E.M. and Apweiler R. Bioinformatics, 2001, 17(9): 847-8. doi: 10.1093/bioinformatics/17.9.847

A new bioinformatics analysis tools framework at EMBL-EBI (2010) Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R Nucleic acids research 2010 Jul, 38 Suppl: W695-9 doi: 10.1093/nar/gkq313

What input does InterProScan accept?

The program accepts a single protein sequence in a recognised sequence format. The full list of sequence formats accepted as input is given in this table: EMBOSS sequence formats

The sequence can either be pasted into the web form or uploaded to the web form in a file.

So how can I use InterProScan with nucleotide input?

Ideally use a gene finding program to find protein coding regions and properly translate your sequence taking account of frame shifts etc. Then use this predicted protein as input to InterProScan.

Is there a limit on the number of sequences or the size of the file that I submit to InterProScan?

The input for InterProScan is limited to 1 sequence or to a 1MB file (whichever is smaller). For batch runs of InterProScan see our web services tools ( or use the stand-alone version of InterProScan.

Where can I find information on the different parameters/options?

The only parameter for InterProScan is the selection of which scanning applications are run against your sequence. For more information on this see the stand-alone Readme file, or the InterPro user manual or help pages.

What output does InterProScan produce?

InterProScan outputs a summary of hits, text and XML files containing the hits, and a graphic showing the hits and where they occur in the sequence.

How do I download the outputs?

The text, XML and graphic output can be downloaded by clicking the download buttons in the results tabs. The graphic can be downloaded in SVG format, or you can right click the image to save as a PNG.

How long are results stored at the EBI?

Results are stored at the EBI for a week from the date of job submission.

Why do I get a 'Raw Tool Output' page?

This happens when we can't parse the results of your InterProScan job - usually because the job has failed for some reason. Have a look at the links on the page, especially the Tool Error Details, for clues as to why this might have happened, and check your input for errors.

Why do I get a 'Job not found' page?

This happens when we can't find the job that you have requested. Normally it's a result of trying to look at the page over a week after the job was submitted, so the data is no longer available at the EBI. If you've copied the URL from a recent email job, check for any mistakes in the link.

Why do I get System command [find] failed error?

This is an intermittant error that rarely occurs when a lot of jobs are using our server at the same time, and means that that particular InterProScan job has not completed properly.

There is nothing permenantly wrong with your sequence or our website when this happens, so the solution is to re-submit the job and it should complete fine the second time. Note that many tools that use InterProScan in the background will automatically re-try failed jobs.

Where can I get further help for InterProScan at the EBI?

For more detailed information see the documentation for the perl stand-alone InterProScan package (Readme file or FAQ's), or the InterPro user manual or help pages.

For specific help about any problems with or if you have any feedback on InterProScan at the EBI please feel free to contact our helpdesk ( ideally including full details about your problem and the URL of the page you are contacting us about.