Please note: Users of Prime 1.2012 and higher do not need to use the PROF or CLUSTALW software in order to increase the accuracy of alignments.

Two distinct third-party secondary structure prediction programs can be used to increase the accuracy of, and get better results from, Prime. One of these programs (SSPRO) is already bundled with Prime and the other (PSIPRED V2.61) may be manually installed by you, at your election, and subject to license terms, if any, applicable to it, by following the link below to the third-party web site where you may download the third-party program and then install it.

Below you will find the link to the third-party web site. If you opted to download the third-party program, please click here for instructions on how to compile and install it.

PSIPRED

The PSIPRED home page is located at:

http://bioinf.cs.ucl.ac.uk/psipred/

and contains information about the program, referrals to terms of use and/or license terms (in the README file), and a link to download the program. Instructions for installing the program for use with Prime can be found here.