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**                                                                                          **
**                                         SNPs&GO                                          **
**                  Predicting disease associated variation using GO terms                  **
**                                                                                          **
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      Sequence File: B9A064.seq

      Mutation     Prediction   RI  Probability   Method
         P115R        Disease    3        0.643   PhD-SNP:  F[P]=99%  F[R]=0%   Nali=179
         P115R        Disease    7        0.874   PANTHER:  F[P]=85%  F[R]=0%  
         P115R        Disease    4        0.679   SNPs&GO

         S123F        Neutral    0        0.500   PhD-SNP:  F[S]=90%  F[F]=0%   Nali=180
         S123F        Disease    7        0.858   PANTHER:  F[S]=70%  F[F]=0%  
         S123F        Neutral    2        0.421   SNPs&GO

         A132D        Disease    6        0.798   PhD-SNP:  F[A]=72%  F[D]=0%   Nali=180
         A132D        Disease    4        0.717   PANTHER:  F[A]=60%  F[D]=1%  
         A132D        Disease    2        0.576   SNPs&GO

         T133K        Disease    5        0.749   PhD-SNP:  F[T]=60%  F[K]=0%   Nali=180
         T133K        Neutral    3        0.355   PANTHER:  F[T]=34%  F[K]=4%  
         T133K        Neutral    4        0.315   SNPs&GO

         L134P        Disease    8        0.875   PhD-SNP:  F[L]=66%  F[P]=0%   Nali=180
         L134P        Disease    7        0.833   PANTHER:  F[L]=45%  F[P]=0%  
         L134P        Disease    4        0.709   SNPs&GO

         L137R        Disease    8        0.914   PhD-SNP:  F[L]=78%  F[R]=0%   Nali=180
         L137R        Disease    4        0.717   PANTHER:  F[L]=46%  F[R]=1%  
         L137R        Disease    6        0.802   SNPs&GO

         V148A        Disease    4        0.680   PhD-SNP:  F[V]=90%  F[A]=0%   Nali=180
         V148A        Disease    2        0.601   PANTHER:  F[V]=66%  F[A]=3%  
         V148A        Disease    1        0.542   SNPs&GO

         W150R        Disease    9        0.928   PhD-SNP:  F[W]=100% F[R]=0%   Nali=180
         W150R        Disease    8        0.883   PANTHER:  F[W]=84%  F[R]=0%  
         W150R        Disease    8        0.889   SNPs&GO

         V161G        Neutral    2        0.423   PhD-SNP:  F[V]=63%  F[G]=0%   Nali=180
         V161G        Neutral    6        0.182   PANTHER:  F[V]=32%  F[G]=12% 
         V161G        Neutral    9        0.056   SNPs&GO

         L180P        Disease    6        0.804   PhD-SNP:  F[L]=99%  F[P]=0%   Nali=180
         L180P        Disease    8        0.892   PANTHER:  F[L]=73%  F[P]=0%  
         L180P        Disease    3        0.672   SNPs&GO

         W187G        Disease    5        0.726   PhD-SNP:  F[W]=76%  F[G]=0%   Nali=180
         W187G        Disease    6        0.805   PANTHER:  F[W]=41%  F[G]=0%  
         W187G        Disease    1        0.550   SNPs&GO

         W187R        Disease    4        0.692   PhD-SNP:  F[W]=76%  F[R]=0%   Nali=180
         W187R        Disease    5        0.774   PANTHER:  F[W]=41%  F[R]=0%  
         W187R        Disease    1        0.559   SNPs&GO

         C195G        Disease    8        0.877   PhD-SNP:  F[C]=100% F[G]=0%   Nali=178
         C195G        Disease   10        0.991   PANTHER:  F[C]=98%  F[G]=0%  
         C195G        Disease    8        0.878   SNPs&GO

         C195W        Disease    8        0.915   PhD-SNP:  F[C]=100% F[W]=0%   Nali=178
         C195W        Disease   10        0.999   PANTHER:  F[C]=98%  F[W]=0%  
         C195W        Disease    8        0.885   SNPs&GO

         V197D        Disease    7        0.839   PhD-SNP:  F[V]=87%  F[D]=0%   Nali=178
         V197D        Disease    7        0.869   PANTHER:  F[V]=66%  F[D]=0%  
         V197D        Disease    6        0.778   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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