Difference between revisions of "Task 3 - Sequence-based predictions"
From Bioinformatikpedia
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* You can log in to the student computer pool: <code>i12k-biolab??.informatik.tu-muenchen.de</code>, where ''??'' goes from 01 to 10 |
* You can log in to the student computer pool: <code>i12k-biolab??.informatik.tu-muenchen.de</code>, where ''??'' goes from 01 to 10 |
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* Or work in the student computer pool. |
* Or work in the student computer pool. |
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+ | |||
+ | == Secondary structure == |
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+ | Use ReProf to predict secondary structure for your protein. Apply ReProf also to these proteins, UniProt IDs: P10775 |
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+ | |||
+ | |||
+ | Give a brief description of the theory and the algorithm, if possible |
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+ | What is predicted? Describe the features in some detail |
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+ | What information is required for the predictions? |
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+ | Apply the prediction methods to your protein and explain how to do this |
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+ | You may try out other protein sequences (this is required when specified) |
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+ | Present, describe and discuss the results |
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+ | Look for other methods, for example here: http://expasy.org/tools/ |
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+ | You may try out more methods |
Revision as of 01:53, 8 May 2012
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