Input |
Protein sequence(s):
- raw sequence
- MSF alignment
- BLC alignment
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Output |
3 state secondary structure prediction, in:
- HTML
- Postscript
- PDF
- Jalview (Java viewer and editor)
- Original ASCII output
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Prediction method |
- Jnet; two fully connected, 3 layer, neural networks, the first with a sliding window of 17 residues predicting the propensity of coil, helix or sheet at each position in a sequence. The second network receives this output and uses a sliding window of 19 residues to further refine the prediction at each position.
- Coils
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Alignments |
- PSI-BLAST scan of a Seg and helixfilt filtered SP/TRMBL database with a 3 iteration scan
- Perform pair-wise comparison of all sequences, to generate percentage identities
- Cluster sequences on basis of percentage identity (complete linkage)
- Remove members with >75% identity
- Remove gaps from the target sequence, and corresponding column beneath that gap, use this alignment for all methods
- Extract PSI-BLAST and HMMPSSM profiles for Jnet
|
Predict |
- Display in coloured HTML, Java, Postscript and PDF
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Consensus |
- Per residue combination of Jent prediction network
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