Difference between revisions of "Sequence-based predictions (PKU)"

Revision as of 14:56, 9 May 2012

Do sequence-based predictions I guess..

Test some SS-predictors ans compare the results to the 'gold standard' of dssp

reprof -i <uniprotID>.fasta
egrep -v "^#|^No" <uniprotID>.reprof |awk '{print $3}'|tr -d '\n' > <uniprotID>_reprof.secstruc

Webserver here

grep Pred: <uniprotID>.psipred_out |cut -d " " -f2|tr -d '\n' > <uniprotID>_psipred.secstruc

Download dssp here and get PDB files matching the Uniprot entries

dssp -i <PDBID>.pdb > <PDBID>.dssp
tail -n+29 <PDBID>.dssp |cut -c17|tr ' ' '-'|tr -d '\n' > <PDBID>_dssp.secstruc

PDB-Files contains only part of the structure or more than 1 chain! e.g. 117aa-424aa for PAH.

@@ Line 10: / Line 10: @@
  reprof -i <uniprotID>.fasta
- grep -v ^# <uniprotID>.reprof |awk '{print $3}'|tr -d '\n' > <uniprotID>_reprof.secstruc
+ egrep -v "^#|^No" <uniprotID>.reprof |awk '{print $3}'|tr -d '\n' > <uniprotID>_reprof.secstruc
 ===PsiPred===