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.
Contents
Introductory talks
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?
- 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, list a few
- You may try out more methods
1. Secondary structure prediction
PSIPRED
- /apps/psipred_2.5 and psipred_3.2
- Script: runpsipred -> adapt paths
- Readme: http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/
- Server: http://bioinf.cs.ucl.ac.uk/psipred/
Jpred3
Comparison with DSSP
- /apps/dssp
- Server: http://swift.cmbi.ru.nl/servers/html/
- http://swift.cmbi.ru.nl/gv/dssp
2. Prediction of disordered regions
DISOPRED
- /apps/disopred_2.4.2.
- Script: rundisopred -> adapt paths
- Server: http://bioinf.cs.ucl.ac.uk/disopred/
POODLE
- Server: http://mbs.cbrc.jp/poodle/poodle.html
- for example, POODLE-I (POODLE series only)
META-Disorder
- man metadisorder
- to be continued...
3. Prediction of transmembrane alpha-helices
Predict transmembrane helices 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 to apply the prediction methods
TMHMM
Phobius
TMtop
4. Prediction of signal peptides
SignalP
TargetP
5. Prediction of GO terms
TMHMM 2.0
