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**                                                                                          **
**                                         SNPs&GO                                          **
**                  Predicting disease associated variation using GO terms                  **
**                                                                                          **
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WARNING: Incorrect mutation S3665Y
WARNING: Incorrect mutation K34R
WARNING: Incorrect mutation Q3299R
WARNING: Incorrect mutation P3340S
WARNING: Incorrect mutation D1232N
WARNING: Incorrect mutation E303D
WARNING: Incorrect mutation Q725H
WARNING: Incorrect mutation S2728Y
WARNING: Incorrect mutation R3046W
WARNING: Incorrect mutation E1228D
WARNING: Incorrect mutation K2067R
WARNING: Incorrect mutation R1751H
WARNING: Incorrect mutation T345N
WARNING: Incorrect mutation K599T
WARNING: Incorrect mutation R847S
WARNING: Incorrect mutation N1002H
WARNING: Incorrect mutation T2427A
WARNING: Incorrect mutation V2736G
WARNING: Incorrect mutation L1346P
WARNING: Incorrect mutation E2633K

      Sequence File: AKAP9_HUMAN.seq

      Mutation     Prediction   RI  Probability   Method
        S2892Y        Disease    5        0.742   PhD-SNP:  F[S]=59%  F[Y]=0%   Nali=16
        S2892Y        Disease    1        0.547   PANTHER:  F[S]=15%  F[Y]=1%  
        S2892Y        Disease    0        0.500   SNPs&GO

        G3507S        Neutral    3        0.355   PhD-SNP:  F[G]=50%  F[S]=5%   Nali=19
        G3507S        Neutral    1        0.474   PANTHER:  F[G]=34%  F[S]=3%  
        G3507S        Neutral    3        0.332   SNPs&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
             PhD-SNP:  SVM input is the sequence and profile at the mutated position
             SNPs&GO:  SVM input is all the input in PhD-SNP, PANTHER  and GO term features
      F[X]: Frequency of residue X in the sequence profile
      Nali: Number of aligned sequences in the mutated site

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**                                                                                          **
**     Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. (2009). Functional    **
**     annotations improve the predictive score of human disease-related mutations in       **
**     proteins. Human Mutation. 30:1237-1244.                                              **
**                                                                                          **
**     Capriotti E, Altman RB. (2011). Improving the prediction of disease-related vari-    **
**     ants using protein three-dimensional structure. BMC Bioinformatics. 12 (Sup.4) S3.   **
**                                                                                          **
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