Protocol

Secondary structure

Sources

The data and scripts we used can be found in /mnt/home/student/angermue/mp/tasks/task03/ss

DSSP assignment

We simply used the DSSP server to get the DSSP secondary structure assignments.

PSIPRED

For calling PSIPRED, we adjusted the script runpsipred of the PSIPRED package. Three rounds PSI-BLAST were carried out to build the PSI-BLAST profile which is used as input of PSIPRED.

Reprof

We called the pre-installed Reprof program by reprof -i FASTA-SEQUENCE -o OUTPUT-FILE.

Helper scripts

ss_format.pl	Converts the output of DSSP, PSIPRED, or Reprof into a common output format with secondary structure states H, E, C.
ss_eval.pl	Takes a reference and further ss_format.pl formatted files which are to be evaluated.
ss_viz.pl	Visualizes several ss_format.pl formatted predictions-