Difference between revisions of "Lab Journal of Task 3 (MSUD)"

From Bioinformatikpedia
(→‎Disordered protein)
m (→‎Disordered protein)
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* '''IUPred'''
  
* '''IUPred'''
−
** Predictions were performed through the web server of IUPred. Graphical profiles of
+
** Predictions were performed through the web server of IUPred. Graphical profiles of the results were downloaded.
  +
** Output of IUPred are stored in the directory <tt>/mnt/home/student/weish/master-practical-2013/task03/02-disordered-protein/iupred</tt>
−
the results were downloaded.
  
−
** Output of IUPred are stored in the directory
 
−
<tt>/mnt/home/student/weish/master-practical-2013/task03/02-disordered-protein/iupred</tt>
  
 
** We have also performed the prediction from command-line, following is the bash script:
  
** We have also performed the prediction from command-line, following is the bash script:
   

Revision as of 19:32, 9 May 2013

Secondary structure

Disordered protein

  • IUPred
    • Predictions were performed through the web server of IUPred. Graphical profiles of the results were downloaded.
    • Output of IUPred are stored in the directory /mnt/home/student/weish/master-practical-2013/task03/02-disordered-protein/iupred
    • We have also performed the prediction from command-line, following is the bash script:

<source lang="bash">

  1. !/bin/sh -e

INPUT=$HOME/master-practical-2013/task03 OUTPUT=$HOME/master-practical-2013/task03/02-disordered-protein/iupred PARAMS="long short glob"

if [ ! -d $OUTPUT ]; then 

       mkdir $OUTPUT

fi

for seq in $INPUT/*.fasta do 

       filename=`basename $seq`
       for param in $PARAMS
       do
               iupred $seq $param > $OUTPUT/iupred_${filename}_$param.tsv
       done

done </source>

Transmembrane helices

Signal peptides

GO terms

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