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

      Mutation     Prediction   RI  Probability   Method
         L125Q        Neutral    1        0.475   PhD-SNP:  F[L]=13%  F[Q]=0%   Nali=167
         L125Q   Unclassified   NA           NA   PANTHER:  F[L]=NA   F[Q]=NA
         L125Q        Neutral    8        0.120   SNPs&GO

         I132V        Neutral    5        0.248   PhD-SNP:  F[I]=40%  F[V]=9%   Nali=193
         I132V   Unclassified   NA           NA   PANTHER:  F[I]=NA   F[V]=NA
         I132V        Neutral    8        0.096   SNPs&GO

         Y160H        Disease    7        0.836   PhD-SNP:  F[Y]=59%  F[H]=1%   Nali=191
         Y160H   Unclassified   NA           NA   PANTHER:  F[Y]=NA   F[H]=NA
         Y160H        Neutral    1        0.427   SNPs&GO

         M170V        Neutral    6        0.220   PhD-SNP:  F[M]=6%   F[V]=8%   Nali=191
         M170V   Unclassified   NA           NA   PANTHER:  F[M]=NA   F[V]=NA
         M170V        Neutral    7        0.137   SNPs&GO

         S232C        Neutral    7        0.171   PhD-SNP:  F[S]=21%  F[C]=1%   Nali=108
         S232C   Unclassified   NA           NA   PANTHER:  F[S]=NA   F[C]=NA
         S232C        Neutral    9        0.040   SNPs&GO

         C264Y        Disease    4        0.691   PhD-SNP:  F[C]=18%  F[Y]=1%   Nali=180
         C264Y   Unclassified   NA           NA   PANTHER:  F[C]=NA   F[Y]=NA
         C264Y        Neutral    2        0.404   SNPs&GO

         G297S        Neutral    4        0.306   PhD-SNP:  F[G]=37%  F[S]=6%   Nali=178
         G297S   Unclassified   NA           NA   PANTHER:  F[G]=NA   F[S]=NA
         G297S        Neutral    8        0.076   SNPs&GO

         L463V        Disease    2        0.588   PhD-SNP:  F[L]=95%  F[V]=2%   Nali=175
         L463V   Unclassified   NA           NA   PANTHER:  F[L]=NA   F[V]=NA
         L463V        Neutral    4        0.285   SNPs&GO

         S536C        Neutral    7        0.156   PhD-SNP:  F[S]=57%  F[C]=0%   Nali=27
         S536C   Unclassified   NA           NA   PANTHER:  F[S]=NA   F[C]=NA
         S536C        Neutral    9        0.025   SNPs&GO

         A540D        Neutral    6        0.215   PhD-SNP:  F[A]=80%  F[D]=10%  Nali=19
         A540D   Unclassified   NA           NA   PANTHER:  F[A]=NA   F[D]=NA
         A540D        Neutral    9        0.055   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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