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**                                                                                          **
**                                         SNPs&GO                                          **
**                  Predicting disease associated variation using GO terms                  **
**                                                                                          **
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      Sequence File: fileseq.seq

      Mutation     Prediction   RI  Probability   Method
          L23I        Neutral    4        0.287   PhD-SNP:  F[L]=100% F[I]=0%   Nali=36
          L23I        Disease    1        0.568   PANTHER:  F[L]=77%  F[I]=4%  
          L23I        Neutral    7        0.149   SNPs&GO

         E129K        Disease    3        0.651   PhD-SNP:  F[E]=71%  F[K]=0%   Nali=34
         E129K        Neutral    2        0.414   PANTHER:  F[E]=59%  F[K]=3%  
         E129K        Neutral    2        0.405   SNPs&GO

         S179T        Neutral    7        0.131   PhD-SNP:  F[S]=86%  F[T]=11%  Nali=35
         S179T        Disease    3        0.636   PANTHER:  F[S]=72%  F[T]=3%  
         S179T        Neutral    8        0.112   SNPs&GO

         I404M        Neutral    7        0.126   PhD-SNP:  F[I]=34%  F[M]=18%  Nali=60
         I404M        Disease    4        0.703   PANTHER:  F[I]=65%  F[M]=1%  
         I404M        Neutral    6        0.222   SNPs&GO

         R414H        Disease    2        0.606   PhD-SNP:  F[R]=67%  F[H]=5%   Nali=62
         R414H        Disease    3        0.628   PANTHER:  F[R]=61%  F[H]=1%  
         R414H        Neutral    1        0.465   SNPs&GO

         T562M        Neutral    4        0.280   PhD-SNP:  F[T]=34%  F[M]=0%   Nali=73
         T562M        Disease    3        0.637   PANTHER:  F[T]=53%  F[M]=1%  
         T562M        Neutral    5        0.261   SNPs&GO

         N818D        Neutral    3        0.326   PhD-SNP:  F[N]=47%  F[D]=0%   Nali=35
         N818D        Neutral    3        0.332   PANTHER:  F[N]=54%  F[D]=4%  
         N818D        Neutral    8        0.122   SNPs&GO

         R945K        Neutral    0        0.491   PhD-SNP:  F[R]=94%  F[K]=0%   Nali=31
         R945K        Disease    2        0.597   PANTHER:  F[R]=80%  F[K]=4%  
         R945K        Neutral    3        0.350   SNPs&GO

         S948P        Neutral    8        0.102   PhD-SNP:  F[S]=25%  F[P]=34%  Nali=31
         S948P        Neutral    8        0.115   PANTHER:  F[S]=34%  F[P]=13% 
         S948P        Neutral   10        0.011   SNPs&GO

        S1400L        Neutral    7        0.168   PhD-SNP:  F[S]=88%  F[L]=0%   Nali=31
        S1400L        Neutral    0        0.499   PANTHER:  F[S]=54%  F[L]=2%  
        S1400L        Neutral    8        0.079   SNPs&GO

        A1755V        Neutral    8        0.081   PhD-SNP:  F[A]=41%  F[V]=0%   Nali=16
        A1755V   Unclassified   NA           NA   PANTHER:  F[A]=NA   F[V]=NA
        A1755V        Neutral   10        0.023   SNPs&GO

        V1804L        Neutral    9        0.063   PhD-SNP:  F[V]=29%  F[L]=0%   Nali=13
        V1804L        Neutral    8        0.094   PANTHER:  F[V]=10%  F[L]=5%  
        V1804L        Neutral   10        0.012   SNPs&GO

        S2029F        Neutral    3        0.347   PhD-SNP:  F[S]=95%  F[F]=0%   Nali=21
        S2029F        Disease    3        0.652   PANTHER:  F[S]=54%  F[F]=1%  
        S2029F        Neutral    7        0.140   SNPs&GO

        W2101G        Disease    3        0.628   PhD-SNP:  F[W]=92%  F[G]=0%   Nali=23
        W2101G        Disease    3        0.643   PANTHER:  F[W]=69%  F[G]=1%  
        W2101G        Neutral    0        0.479   SNPs&GO

        A2121V        Neutral    4        0.275   PhD-SNP:  F[A]=79%  F[V]=0%   Nali=23
        A2121V        Neutral    2        0.394   PANTHER:  F[A]=57%  F[V]=3%  
        A2121V        Neutral    8        0.092   SNPs&GO

        S2627Y        Neutral    7        0.144   PhD-SNP:  F[S]=47%  F[Y]=0%   Nali=16
        S2627Y   Unclassified   NA           NA   PANTHER:  F[S]=NA   F[Y]=NA
        S2627Y        Neutral   10        0.024   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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