Task 3 - Sequence-based predictions 2011

From Bioinformatikpedia

In contrast to the vast amount of known protein sequences, information about structure and function is available for only very few proteins. Sequence-based predictions of protein features aim to decrease this gap.



Introductory talks

Talk on sequence feature prediction: Talk_Task3.pdf

The talk introduced the prediction of:

  • secondary structure
  • disorder
  • transmembrane helices and signal peptides
  • GO terms

Tasks and questions

For each prediction, carry out these assignments and answer these questions:

  • Collect basic information about the methods: author, year, reference
  • Give a brief description of the theory and the algorithm, if possible
  • What is predicted? Describe the features in some detail
  • What information is required for the predictions?
  • Apply the prediction methods to your protein and explain how to do this
  • You may try out other protein sequences (this is required when specified)
  • Present, describe and discuss the results
  • Look for other methods, for example here: http://expasy.org/tools/
  • You may try out more methods


1. Secondary structure prediction

PSIPRED

PSIPRED (with hints on running psipred locally)


Jpred3

Jpred3


Comparison with DSSP

DSSP

2. Prediction of disordered regions

DISOPRED

DISOPRED (with hints on running psipred locally)


POODLE


IUPRED


META-Disorder

  • Do not run locally. If you are interested, have a look at "man metadisorder" in the VM
  • You can use the PredictProtein server for the prediction

3. Prediction of transmembrane alpha-helices and signal peptides

  • Predict transmembrane helices and signal peptides additionally for the following proteins: BACR_HALSA, RET4_HUMAN, INSL5_HUMAN, LAMP1_HUMAN and A4_HUMAN
  • You can look for other alpha-helical transmembrane proteins and proteins with different signal peptides to apply the prediction methods
  • Why is the prediction of transmembrane helices and signal peptides grouped together here?
  • Describe different signal peptides


TMHMM

  • in /apps/tmhmm-2.0c/bin: adapt paths in tmhmm, tmhmm.ORIG and tmhmmformat.pl (/usr/local/bin/ -> /usr/bin/)


Phobius and PolyPhobius


OCTOPUS and SPOCTOPUS


SignalP

  • in /apps/signalp-3.0/signalp: adapt path
  • run as superuser


TargetP


4. Prediction of GO terms

  • Use also the additional proteins from the transmembrane/signal peptide prediction


GOPET


Pfam


ProtFun 2.2