First, a bit of background..
It's been a while in development but finally we are ready to make InterProScan v5 the official release of InterProScan, meaning that v4.x will be retired. The development of InterProScan 5 was motivated by several factors - both feedback from our users and internal needs to have a robust pipeline for keeping all the calculations of InterPro signatures against UniProtKB proteins up-to-date.
As explained on the Google Code wiki for InterProScan 5, there are numerous differences between the two versions, most notably the change from a Perl-based architecture to a Java-based one. We've also simplified the installation process, added a new analysis type (Phobius), improved the output formats that users can get their results in and tailored this version to work on a large-scale better than ever before.
In order to help users transition from using v4 to v5, we have created a page on our Google Code wiki that explains what might need to be changed to migrate from using v4 to v5. In the initial version of the page (which will be added to as and when we get requests from users for clarification) we describe changes to the command-line options available and the output formats generated. This is mainly of interest to users who have downloaded InterProScan and installed it locally.
Migrating from v4 to v5
Changes will also be reflected in the EBI-hosted versions, with both the web interface and SOAP/REST web services changing to v5 shortly. We will continue to run the hosted InterProScan v4.8 in parallel with the v5 whilst people swtich over but the older version will no longer be actively developed (including releases of data).
It is our intention to officially launch InterProScan 5 with the next public release of the InterPro database, currently scheduled for 19th September 2013.
If people have any questions about the above or suggestions, please contact us