Difference between revisions of "Task 3 - Sequence-based predictions"
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− | Use fasta sequences for the prediction. You can find out about Reprof usage by running <code>reprof</code> or reading the man page (<code>man reprof</code>). |
+ | Use fasta sequences for the prediction. You can find out about Reprof usage by running <code>reprof</code> or reading the man page (<code>man reprof</code>). Peter Hoenigschmig (<code>hoenigschmid@rostlab.org</code>) would like to hear about anything that would improve the description or if anything seems unclear. For help, you can always ask us first. |
Compare the ReProf results to [http://bioinf.cs.ucl.ac.uk/psipred/ PsiPred] and [ http://mrs.cmbi.ru.nl/hsspsoap/ DSSP server] ([http://swift.cmbi.ru.nl/gv/dssp/ DSSP]). Before you use DSSP, find out more about the example proteins (and yours) using UniProt and the PDB. |
Compare the ReProf results to [http://bioinf.cs.ucl.ac.uk/psipred/ PsiPred] and [ http://mrs.cmbi.ru.nl/hsspsoap/ DSSP server] ([http://swift.cmbi.ru.nl/gv/dssp/ DSSP]). Before you use DSSP, find out more about the example proteins (and yours) using UniProt and the PDB. |
Revision as of 02:29, 8 May 2012
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
- You can log in to the student computer pool:
i12k-biolab??.informatik.tu-muenchen.de
, where ?? goes from 01 to 10. - Work in the student computer pool.
- You can also install the programs on your own computer.
Secondary structure
Use ReProf to predict secondary structure for your protein. Apply ReProf also to these proteins:
- P10775
- Q9X0E6
- Q08209
Use fasta sequences for the prediction. You can find out about Reprof usage by running reprof
or reading the man page (man reprof
). Peter Hoenigschmig (hoenigschmid@rostlab.org
) would like to hear about anything that would improve the description or if anything seems unclear. For help, you can always ask us first.
Compare the ReProf results to PsiPred and [ http://mrs.cmbi.ru.nl/hsspsoap/ DSSP server] (DSSP). Before you use DSSP, find out more about the example proteins (and yours) using UniProt and the PDB.
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