Difference between revisions of "Sequence-based predictions HEXA"
From Bioinformatikpedia
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== Secondary Structure Prediction == |
== Secondary Structure Prediction == |
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| − | == Prediction of disordered regions == |
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| − | * DISOPRED |
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| − | Authors: Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT. |
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| − | Year: 2004 |
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| − | Source: [[http://www.ncbi.nlm.nih.gov/pubmed/15019783 Prediction and functional analysis of native disorder in proteins from the three kingdoms of life.]] |
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| − | Description: |
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| − | This method is based on a neuronal network which was trained on high resolution X-ray structures from PDB. Disordered regions are regions, which appears in the sequence record, but their electrons are missing from electronic density map. This approach can also failed, because missing electrons can also arise because of the cristallization process. |
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| − | The method runs first a PsiBlast search against a filtered sequence database. Next, a profile for each residue is calculated and classified by using the trained neuronal network. |
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| − | Prediction: |
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| − | As a prediction result you get a file with the predicted disordered region, the precision and recall. Furthermore you can a more detailed output. There you see the sequence, and the predictions and also numbers above the sequence (from 0 to 9 which shows you how likly your prediction is) |
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| − | Input: |
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| − | If you run disopred on the console, you have to define the location of your database. The program needs as input your sequence in a file with fasta format. |
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| − | *POODLE |
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| − | Prediction of order and disorder by machine-learning |
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| − | Authors: S. Hirose, K. Shimizu, S. Kanai, Y. Kuroda and T. Noguchi |
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| − | Year: 2007 |
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| − | There exist three different variants of POODLE. |
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| − | The first variant is called POODLE-L which predicts mainly long disorder region with a length more than 40. |
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| − | Source: [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17545177&ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions.]] |
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| − | The next variant is called POODLE-S, which predicts mainly short disorder regions. |
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| − | Source: [[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17599940&ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix.]] |
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| − | The last variant is called POODLE-I, which integrates structal information predictors. |
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| − | Source: [[http://www.bioinfo.de/isb/2010/10/0015/ POODLE-I: Disordered region prediction by integrating POODLE series and structural information predictors based on a workflow approach]] |
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| − | There exists als another variant called POODLE-W, which compares different sequences and predicts which sequence is the most disordered one, but this method wasn't used in our analysis. |
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| − | Description: |
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| − | POODLE is also a machine learning based method. This method based on a 2-level SVM (Support Vector Machine). |
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| − | We describe here the POODLE-L in detail, but all POODLE variants use the same principle. |
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| − | The method was trained on disordered proteins and proteins with no disoredered regions. On the first level, the SVM predicts the probability of a 40-residue sequence segment to be disordered. If the algorithm found such a disordered regions, the second level of the SVM use the output from the first level and predicts the probability to be disordered for each amino acid. |
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| − | Output: |
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| − | The result of this method is a file with the single amino acids, the prediction if it is ordered or not and the probability for the state. Furtheremore, you get a graphical view of the result. |
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| − | Input: |
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| − | We used the POODLE webserver for our analysis. We paste our sequence in fasta format in the input window and chose the POODLE variant. |
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== Prediction of transmembrane alpha-helices and signal peptides == |
== Prediction of transmembrane alpha-helices and signal peptides == |
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Revision as of 15:31, 27 May 2011
Contents
- 1 General Information
- 2 Secondary Structure Prediction
- 3 Prediction of transmembrane alpha-helices and signal peptides
- 4 Prediction of GO terms
- 5 Secondary Structure prediction
- 6 Prediction of disordered regions
- 7 Prediction of transmembrane alpha-helices and signal peptides
- 8 Prediction of GO terms
General Information
Secondary Structure Prediction
Prediction of transmembrane alpha-helices and signal peptides
Prediction of GO terms
Secondary Structure prediction
Prediction of disordered regions
- Disopred
Disopred predicts two disordered regions in our protein. The first region is at the beginning of the protein (first two residues) and the second region is at the end (last three regions). This prediction is probably wrong, because it is normal, that the electrons from the first and the last amino acids lack in the electron density map. So, our protein Hexosamidase A has no disordered regions.
- POODLE
We decided to test several POODLE variants and to compare the results.
POODLE-I
POODLE-I predicted five disordered regions:
| start position | end position | length |
| 1 | 2 | 2 |
| 14 | 19 | 6 |
| 83 | 89 | 7 |
| 105 | 109 | 5 |
| 527 | 529 | 3 |
POODLE-L
POODLE-L found no disordered regions. Therefore, there is no disordered region with a length more than 40aa in our protein.
POODLE-S (High B-factor residues)
TODO
POODLE-S predicted five disordered regions:
| start position | end position | length |
| 0 | 2 | 2 |
| 13 | 19 | 7 |
| 83 | 88 | 6 |
| 105 | 109 | 5 |
| 526 | 529 | 4 |
POODLE-S (missing residues)
POODLE-S (missing residues) predicts regions as disordered, if there is a amino acid in the sequence record, but not on the electron density map.
Poodle-S found 6 disordered regions.
| start position | end position | length |
| 17 | 18 | 2 |
| 53 | 61 | 9 |
| 78 | 109 | 33 |
| 153 | 153 | 1 |
| 280 | 280 | 1 |
| 345 | 345 | 1 |
Graphical Output:
TODO Comparison!!!
