SNPs&GO
 
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SNPs&GO3d
Predicting disease associated variations using GO terms


PDB File: pdb1cdf.spdb    Chain: A
Alignment File: pdb1cdf.spdb.blast
GO-terms File: pdb1cdf.spdb.seq.go
Output File: output.txt




Mutation
Prediction
RI
Probability
Method

Disease
7
0.828
S3D-PROF: F[C]=100% F[Q]=0% Nali=51 RSA=8
 
Disease
8
0.887
PANTHER: F[C]=80% F[Q]=0%
 
Disease
9
0.925
SNPs&GO
 
Disease
9
0.960
S3Ds&GO
 
Disease
8
0.880
S3D-PROF: F[C]=100% F[R]=0% Nali=87 RSA=14
 
Disease
10
0.977
PANTHER: F[C]=94% F[R]=0%
 
Disease
10
0.975
SNPs&GO
 
Disease
9
0.970
S3Ds&GO
 
Neutral
9
0.048
S3DPROF: F[S]=10% F[L]=8% Nali=85 RSA=86
 
Neutral
8
0.106
PANTHER: F[S]=10% F[L]=15%
 
Neutral
6
0.148
SNPs&GO
 
Neutral
5
0.231
S3Ds&GO



Mutation: WT+POS+NEW
    WT: Residue in wild-type protein
    POS: Residue position
    NEW: New residue after mutation

Prediction:
    Neutral: Neutral variation
    Disease: Disease associated variation

RI: Reliability Index

Probability: Disease probability (if >0.5 mutation is predicted Disease)

Method: SVM type and data
    PANTHER: Output of the PANTHER algorithm
    S3D-PROF: SVM input is the protein structure and profile at the mutated position
    SNPs&GO: Standard sequence-based SNPs&GO method.
    S3Ds&GO: SVM input is all the input in S3D-PROF, PANTHER and GO terms

F[X]: Frequency of residue X in the sequence profile
Nali: Number of aligned sequences in the mutated site
RSA: Relative Solvent Accesible Area
 
 
 
 
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