The EBI hosts an excellent tool called InterProScan, for finding conserved domains in protein sequences. Even better, there’s a SOAP-based web service and associated perl script, allowing you to submit sequences from the command line.
The only problem is that the script requires SOAP::Lite version 0.60 to work. SOAP::Lite on my machine is the latest, 0.69. Fortunately, Perl allows you to install older module versions in a special place, away from the others. All you need to do is:
- Use CPAN to install the module “only” (only.pm)
- Download the old module version that you want from CPAN
- Unpack the tarball and run “perl Makefile.PL”, “make” and optionally “make test”, as usual
- Now run “sudo perl -Monly=install”, instead of “sudo make install”
You should see lines of output such as:
where version-lib/0.60 is the special location for older versions.
Finally, include a line like this in your Perl:
use only SOAP::Lite => '0.60';
It would be nice if web service maintainers kept their scripts up to date with the newest module versions – but this is the next best solution.