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PSI-BLAST PSSM

Original sets of parameters for PSIPRED, DISOPRED and MEMSAT-SVM

• MEMSAT-SVM: invoke the program with the option -mtx 1 and make sure that the input file is a PSI-BLAST result blastpgp-parameters: -b 0 -j 2 -h 0.001 -e 0.001
• PSIPRED: apply patch and provide pre-computed PSI-BLAST result as second input blastpgp-parameters: -b 0 -j 3 -h 0.001 -v 5000
• DISOPRED3: apply patch and provide pre-computed PSI-BLAST result as second input blastpgp-parameters: -b 0 -j 3 -h 0.001

PSI-BLAST predictions

We have now three packages on biocore for the three programs PSIPRED, DISOPRED, MEMSAT-SVM. Install them as follows conda install -c biocore memsat-svm disopred psipred, you might need to add biocore as an anaconda channel conda config --add channels bioconda.

All three programs should have the same command line arguments to re-use pre-computed PSI-BLAST results. Raise the flag -mtx=1 and use your psi-blast result file as input file. Furthermore, there is no longer the need to manually change any path names in the wrapper programs. Everything should be configurable by arguments.