Difference between revisions of "Protocol"
From Bioinformatikpedia
(Created page with "== Secondary structure == === Sources === The data and scripts we used can be found in <tt>/mnt/home/student/angermue/mp/tasks/task03/ss</tt> === DSSP assignment === We simply u…") |
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We called the pre-installed Reprof program by <tt>reprof -i FASTA-SEQUENCE -o OUTPUT-FILE</tt>. |
We called the pre-installed Reprof program by <tt>reprof -i FASTA-SEQUENCE -o OUTPUT-FILE</tt>. |
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− | === |
+ | === Further scripts === |
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{| |
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| <tt>ss_format.pl</tt> || Converts the output of DSSP, PSIPRED, or Reprof into a common output format with secondary structure states H, E, C. |
| <tt>ss_format.pl</tt> || Converts the output of DSSP, PSIPRED, or Reprof into a common output format with secondary structure states H, E, C. |
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| <tt>ss_viz.pl</tt> || Visualizes several <tt>ss_format.pl</tt> formatted predictions- |
| <tt>ss_viz.pl</tt> || Visualizes several <tt>ss_format.pl</tt> formatted predictions- |
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+ | |} |
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+ | |||
+ | == Disorder == |
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+ | === Sources === |
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+ | The data and scripts we used can be found in <tt>/mnt/home/student/angermue/mp/tasks/task03/disorder</tt> |
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+ | |||
+ | === IUPred === |
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+ | We called IUPred by: |
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+ | <pre> |
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+ | iupred SEQ-FILE long |
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+ | </pre> |
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+ | |||
+ | === Further scripts === |
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+ | {| |
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+ | | <tt> eval.pl </tt> || Calculates the precision, sensitivity, and specificity given a set of predicted residues, reference residues and the length of the protein. |
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Revision as of 08:56, 18 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. |