Lab Journal of Task 3 (MSUD)

For task 3 we have used the reference sequence of BCKDHA and other given example proteins.

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>

MetaDisorder(MD)

• As the man page of metadisorder describes, the prediction of disordered region is based on the results of other programs such as NORSnet, PROFbval etc. Rather than directly call metadisorder we have used the wrapper program predictprotein as is described on the exercise page.
• Comparison to DisProt database: TODO

Following script was called for the task: <source lang="bash">

1. !/bin/sh -e

INPUT=$HOME/master-practical-2013/task03 OUTPUT=$HOME/master-practical-2013/task03/metadisorder EXE=predictprotein

1. make output directory

if [ ! -d $OUTPUT ]; then

       mkdir $OUTPUT

fi

1. call metadisorder for all query sequences

for seq in $INPUT/*.fasta do

       filename=`basename $seq`
       $EXE --seqfile $seq --target metadisorder -p metadisorder_$filename \
       -o $OUTPUT

done echo Done! </source>