Sequence-based predictions (PKU)

From Bioinformatikpedia
Revision as of 12:07, 9 May 2012 by Boidolj (talk | contribs)

Short Task Description

Do sequence-based predictions I guess..

Secondary Structure Prediction

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

ReProfSeq

reprof -i <uniprotID>.fasta
grep -v ^# <uniprotID>.reprof |awk '{print $3}'|tr -d '\n' > <uniprotID>_reprof.secstruc

PsiPred

Webserver here

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

DSSP

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.