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Meta-SNP
Meta-predictor of disease causing variants
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Required Input
Meta-SNP have been optimized to predict if a given single point
protein variation can be classified as disease associated or
polymorphism. Meta-SNP requires in input:
- Protein Sequence:
Protein Sequence: Meta-SNP server requires the protein
sequence that can be provided in three different ways:
1) raw or fasta format,
2) uploading a text file containing the protein
sequence. The server first checks the Protein Sequence box, if no
sequence is provided it then checks if a text file has been uploaded.
- Mutation: the server requires a
list of comma separated mutations in the XPOSY format where X and Y
are the wild-type and mutant residues respectively, and POS is
the number of the mutated position in the sequence.
The results of Meta-SNP algorithm can be sent
to your e-mail address filling the appropriate box or displayed
interactively if you do not enter any e-mail address.
Output
The output consists of a table listing the number of the mutated
position in the protein sequence, the wild-type residue, the new
residue and the predicions of the 4 predictors (PATHER, PhD-SNP, SIFT
and SNAP).
The mutation is classified as disease-related
(Disease)
or polymorphism (Neutral).
Under the prediction of each method the values returned by them is
reported.
The server also disply the RI value (Reliability Index)
that is calculated from the output Meta-SNP output O as:
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More details about the output of the server are reported below.
Mutation: WT+POS+NEW
WT: Residue in wild-type protein
POS: Residue position
NEW: New residue after mutation
Prediction:
Neutral: Neutral variants
Disease: Disease causing variants
Outputs: Value reported under each prediction
PANTHER: Between 0 and 1. (If >0.5 mutation is predicted Disease)
PhD-SNP: Between 0 and 1.(If >0.5 mutation is predicted Disease)
SIFT: Positive Value (If >0.05 mutation is predicted Neutral)
SNAP: Output normalized between 0 and 1 (If >0.5 mutation is predicted Disease)
Meta-SNP:Between 0 and 1. (If >0.5 mutation is predicted Disease)
RI: Reliability Index between 0 and 10.
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