Difference between revisions of "Sequence-based predictions TSD"
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== Transmembrane helices == |
== Transmembrane helices == |
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== Signal peptides == |
== Signal peptides == |
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| + | Proteins: [http://www.uniprot.org/uniprot/P02768 P02768], [http://www.uniprot.org/uniprot/P11279 P11279], [http://www.uniprot.org/uniprot/P47863 P47863] |
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| + | <br> |
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| + | SignalP employs 3 main scores for the prediction of signal peptides, C, S and Y. The S-score stands for the actual signal peptide prediction, with high scores indicating that the corresponding amino acid is part of a signal peptide, and low scores indicating that the amino acid is part of a mature protein. |
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| + | The C-score is the cleavage score, which indicates the best cleavage cite when significantly high. (When a cleavage site position is referred to by a single number, the number indicates the first residue in the mature protein.) |
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| + | Y-max is a derivative of the C-score combined with the S-score calculated to give a better cleavage site prediction than the raw C-score alone. |
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| + | |||
| + | There are two additional scores reported in the SignalP output, namely the S-mean and the D-score. The S-mean is the average of the S-score, ranging from the N-terminal amino acid to the amino acid assigned with the highest Y-max score. The D-score is implemented as a weighted average of the S-mean and the Y-max scores. |
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| + | |||
| + | For non-secretory proteins all scores are supposed to be very low. |
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| + | |||
== GO terms == |
== GO terms == |
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=== GOpet === |
=== GOpet === |
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Revision as of 15:10, 14 May 2012
Thor: He's my brother
Natasha Romanoff: He killed 80 people in 2 days
Thor: ...He's adopted
If not noted otherwise, the sequence for all predictions is the HEXA Reference sequence. A protocol for this task can be found here.
Contents
Secondary structure
Disorder
Transmembrane helices
Signal peptides
Proteins: P02768, P11279, P47863
SignalP employs 3 main scores for the prediction of signal peptides, C, S and Y. The S-score stands for the actual signal peptide prediction, with high scores indicating that the corresponding amino acid is part of a signal peptide, and low scores indicating that the amino acid is part of a mature protein.
The C-score is the cleavage score, which indicates the best cleavage cite when significantly high. (When a cleavage site position is referred to by a single number, the number indicates the first residue in the mature protein.)
Y-max is a derivative of the C-score combined with the S-score calculated to give a better cleavage site prediction than the raw C-score alone.
There are two additional scores reported in the SignalP output, namely the S-mean and the D-score. The S-mean is the average of the S-score, ranging from the N-terminal amino acid to the amino acid assigned with the highest Y-max score. The D-score is implemented as a weighted average of the S-mean and the Y-max scores.
For non-secretory proteins all scores are supposed to be very low.
GO terms
GOpet
<figtable id="tab:gopetgo">
| GO-Term ID | Type | Confidence | GO-Term description |
|---|---|---|---|
| GO:0003824 | Molecular function | 97% | catalytic activity |
| GO:0004563 | Molecular function | 96% | beta-N-acetylhexosaminidase activity |
| GO:0015929 | Molecular function | 96% | hexosaminidase activity |
| GO:0016787 | Molecular function | 96% | hydrolase activity |
| GO:0016798 | Molecular function | 96% | hydrolase activity acting on glycosyl bonds |
| GO:0004553 | Molecular function | 96% | hydrolase activity hydrolyzing O-glycosyl compounds |
| GO:0016799 | Molecular function | 77% | hydrolase activity hydrolyzing N-glycosyl compounds |
| GO:0046982 | Molecular function | 61% | protein heterodimerization activity |
Table TODO: </figtable>
