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

From Bioinformatikpedia
(Created page with "== Secondary structure == == Disordered protein == == Transmembrane helices == == Signal peptides == == GO terms ==")
 
(→‎Disordered protein)
Line 2: Line 2:
   
 
== Disordered protein ==
  
== 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
  +
<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:
  +
  +
<source lang="bash">
  +
#!/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 ==
  
== Transmembrane helices ==

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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