Task 3 - Sequence-based predictions

Under construction

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. Many sequence-based preditiction methods use evolutionary information, i.e. sequence similiarity. Sequence alignments are therefore often a prerequisite for the predictions.

Theoretical background talks

The introductory talks will give an introduction to sequence-based protein predictions. In particular:

• secondary structure
• disorder
• transmembrane helices
• GO terms

Where to run the jobs

• On your own computers.
• You can log in to the student computer pool: i12k-biolab??.informatik.tu-muenchen.de, where ?? goes from 01 to 10
• Or work in the student computer pool.

Secondary structure

Use ReProf to predict secondary structure for your protein. Apply ReProf also to these proteins, UniProt IDs: P10775

   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