The data and scripts we used can be found in /mnt/home/student/angermue/mp/tasks/task03/ss
We simply used the DSSP server to get the DSSP secondary structure assignments.
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.
We called the pre-installed Reprof program by reprof -i FASTA-SEQUENCE -o OUTPUT-FILE.
|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-|
The data and scripts we used can be found in /mnt/home/student/angermue/mp/tasks/task03/disorder
We called IUPred by:
iupred SEQ-FILE long
|eval.pl||Calculates the precision, sensitivity, and specificity given a set of predicted residues, reference residues and the length of the protein.|
At first, get all the sequences from Uniprot:
wget http://www.uniprot.org/uniprot/P04062.fasta wget http://www.uniprot.org/uniprot/P35462.fasta wget http://www.uniprot.org/uniprot/Q9YDF8.fasta wget http://www.uniprot.org/uniprot/P47863.fasta
Then execute the following bash shell script to do prediction:
#!/bin/bash #$ -S /bin/sh IN=/mnt/project/pracstrucfunc12/data/index_pp/uniprot_sprot.idx DB=/mnt/project/pracstrucfunc12/data/swissprot/uniprot_sprot PATH=$PATH:/mnt/project/pracstrucfunc12/polyphobius/ export PATH mkdir -p output/ for file in `ls | grep ".fasta"`; do `perl /mnt/project/pracstrucfunc12/polyphobius/blastget -db $DB -ix $IN $file > output/$file.blast` wait `/mnt/opt/T-Coffee/bin/kalign -f fasta -input output/$file.blast -output output/$file.msa` wait `perl /mnt/project/pracstrucfunc12/polyphobius/jphobius -poly output/$file.msa &> output/$file.phob` wait done
The SignalP server with version 4.0 was used.