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

Revision as of 12:07, 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
grep -v ^# <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 2: / Line 2: @@
 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 [http://bioinf.cs.ucl.ac.uk/psipred/ here]
+ grep Pred: <uniprotID>.psipred_out |cut -d " " -f2|tr -d '\n' > <uniprotID>_psipred.secstruc
+===DSSP===
+Download dssp [http://swift.cmbi.ru.nl/gv/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.