Difference between revisions of "Protocol"
From Bioinformatikpedia
| Line 35: | Line 35: | ||
| <tt> eval.pl </tt> || Calculates the precision, sensitivity, and specificity given a set of predicted residues, reference residues and the length of the protein. |
| <tt> eval.pl </tt> || Calculates the precision, sensitivity, and specificity given a set of predicted residues, reference residues and the length of the protein. |
||
|} |
|} |
||
| + | |||
| + | == Transmembrane helices == |
||
| + | |||
| + | == Signal peptides == |
||
| + | |||
| + | == GO terms == |
||
Revision as of 15:14, 20 May 2012
Contents
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.
Further 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- |
Disorder
Sources
The data and scripts we used can be found in /mnt/home/student/angermue/mp/tasks/task03/disorder
IUPred
We called IUPred by:
iupred SEQ-FILE long
Further scripts
| eval.pl | Calculates the precision, sensitivity, and specificity given a set of predicted residues, reference residues and the length of the protein. |
