Difference between revisions of "Sequence-based predictions (PKU)"
From Bioinformatikpedia
(→ReProfSeq) |
(→DSSP) |
||
| Line 23: | Line 23: | ||
PDB-Files contains only part of the structure or more than 1 chain! e.g. 117aa-424aa for PAH. |
PDB-Files contains only part of the structure or more than 1 chain! e.g. 117aa-424aa for PAH. |
||
| + | |||
| + | Aligned structure to sequence manually.. |
||
| + | |||
| + | Script to calculate Q3 and SOV: [[Collection_of_scripts#ss_score.py|ss_score.py]] |
||
Revision as of 17:00, 9 May 2012
Contents
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
egrep -v "^#|^No" <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.
Aligned structure to sequence manually..
Script to calculate Q3 and SOV: ss_score.py
