Prottest

 

The portlet allows to submit a single instance of ProtTest to a remote Grid site.

ProtTest was the first program developed for the selection of best-fit models of protein evolution. It is an open source java program to find the best model of amino acid replacement for a given protein alignment.

It is based on the Phyml program for the Maximum Likelihood (ML) optimizations, modified to support +F and four extra substitution matrices and uses the PAL library for handling protein alignments and trees.

Current version of the portlet submits an script to control prottest execution plus the input data. As the application itself is quite big, it is not transmitted together with the input data but downloaded directly from a Storage Element on the remote size. this process is performed by the control script.

Then, after the application has been executed on a serial way, the output results are compressed and returned to the Science Gateway server so the user can download them.