Friday, 2 August 2013

Migrating from InterProScan v4.x to InterProScan v5

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.

Migrating from v4 to v5

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.

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

Thursday, 1 August 2013

InterPro 43.1 is released, fixing the previous data problems

Good news!

Last week we were able to finally release an update to release 43 to fix the problems we identified.

43.1 contains the same member databases as v43.0 (i.e. an upgrade to Pfam from v26.0 to v27.0 compared with the InterPro 42.0 release) but there are 2 main differences:
  1. The pre-calculated match information we supply via the InterPro website and the downloadable match_complete.xml file that is used by InterProScan is now correct
  2. Additional Pfam signatures have been integrated into InterPro entries since v43.0.  This is why in the release notes for 43.1, 13579/14831 Pfam signatures belong to an InterPro entry but in 43.0 only 13079/14831 signatures were included.  (Our curators have been busy!)
We  apologise again for this problem and the inconvenience it might have caused our users.  We have now put in place measures to ensure that this particular problem won't happen again.