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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
          A14V        Neutral    7        0.137   PhD-SNP:  F[A]=17%  F[V]=22%  Nali=366
          A14V        Neutral    8        0.076   PANTHER:  F[A]=11%  F[V]=13% 
          A14V        Neutral    9        0.026   SNPs&GO

         D111A        Disease    1        0.567   PhD-SNP:  F[D]=18%  F[A]=2%   Nali=879
         D111A        Neutral    4        0.306   PANTHER:  F[D]=32%  F[A]=4%  
         D111A        Neutral    4        0.306   SNPs&GO

         D124N        Neutral    1        0.440   PhD-SNP:  F[D]=7%   F[N]=1%   Nali=936
         D124N        Neutral    0        0.494   PANTHER:  F[D]=67%  F[N]=3%  
         D124N        Disease    1        0.564   SNPs&GO

         S129F        Disease    4        0.688   PhD-SNP:  F[S]=27%  F[F]=2%   Nali=943
         S129F        Disease    5        0.732   PANTHER:  F[S]=59%  F[F]=0%  
         S129F        Disease    5        0.742   SNPs&GO

         Y227C        Disease    5        0.742   PhD-SNP:  F[Y]=34%  F[C]=1%   Nali=892
         Y227C        Disease    7        0.847   PANTHER:  F[Y]=66%  F[C]=0%  
         Y227C        Disease    4        0.720   SNPs&GO

         L228V        Neutral    3        0.342   PhD-SNP:  F[L]=51%  F[V]=11%  Nali=928
         L228V        Neutral    3        0.369   PANTHER:  F[L]=65%  F[V]=5%  
         L228V        Neutral    4        0.301   SNPs&GO

         E244V        Neutral    6        0.189   PhD-SNP:  F[E]=12%  F[V]=2%   Nali=952
         E244V        Neutral    4        0.291   PANTHER:  F[E]=15%  F[V]=2%  
         E244V        Neutral    9        0.046   SNPs&GO

         R282H        Neutral    5        0.275   PhD-SNP:  F[R]=4%   F[H]=1%   Nali=884
         R282H   Unclassified   NA           NA   PANTHER:  F[R]=NA   F[H]=NA
         R282H        Neutral    7        0.132   SNPs&GO

         D287N        Disease    0        0.505   PhD-SNP:  F[D]=20%  F[N]=2%   Nali=964
         D287N        Neutral    4        0.283   PANTHER:  F[D]=40%  F[N]=5%  
         D287N        Neutral    5        0.255   SNPs&GO

         E346Q        Neutral    8        0.094   PhD-SNP:  F[E]=3%   F[Q]=19%  Nali=983
         E346Q        Neutral    5        0.227   PANTHER:  F[E]=26%  F[Q]=5%  
         E346Q        Neutral    9        0.054   SNPs&GO

         R484H        Neutral    5        0.256   PhD-SNP:  F[R]=5%   F[H]=1%   Nali=662
         R484H   Unclassified   NA           NA   PANTHER:  F[R]=NA   F[H]=NA
         R484H        Neutral    7        0.161   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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