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**                                                                                          **
**                                         SNPs&GO                                          **
**                  Predicting disease associated variation using GO terms                  **
**                                                                                          **
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WARNING: Incorrect mutation R2323P
WARNING: Incorrect mutation P2500A
WARNING: Incorrect mutation S2501P

      Sequence File: fileseq.seq

      Mutation     Prediction   RI  Probability   Method
         A543G        Neutral    9        0.060   PhD-SNP:  F[A]=17%  F[G]=13%  Nali=23
         A543G   Unclassified   NA           NA   PANTHER:  F[A]=NA   F[G]=NA
         A543G        Neutral   10        0.022   SNPs&GO

         G544A        Neutral    9        0.063   PhD-SNP:  F[G]=33%  F[A]=13%  Nali=23
         G544A   Unclassified   NA           NA   PANTHER:  F[G]=NA   F[A]=NA
         G544A        Neutral   10        0.015   SNPs&GO

         R545P        Neutral    1        0.454   PhD-SNP:  F[R]=39%  F[P]=4%   Nali=22
         R545P   Unclassified   NA           NA   PANTHER:  F[R]=NA   F[P]=NA
         R545P        Neutral    7        0.146   SNPs&GO

         A547P        Neutral    4        0.314   PhD-SNP:  F[A]=13%  F[P]=0%   Nali=22
         A547P   Unclassified   NA           NA   PANTHER:  F[A]=NA   F[P]=NA
         A547P        Neutral    8        0.079   SNPs&GO

         V549L        Neutral    8        0.079   PhD-SNP:  F[V]=19%  F[L]=10%  Nali=20
         V549L   Unclassified   NA           NA   PANTHER:  F[V]=NA   F[L]=NA
         V549L        Neutral   10        0.024   SNPs&GO

         A551P        Neutral    2        0.413   PhD-SNP:  F[A]=22%  F[P]=4%   Nali=22
         A551P   Unclassified   NA           NA   PANTHER:  F[A]=NA   F[P]=NA
         A551P        Neutral    7        0.136   SNPs&GO

         R552P        Disease    2        0.585   PhD-SNP:  F[R]=26%  F[P]=4%   Nali=22
         R552P   Unclassified   NA           NA   PANTHER:  F[R]=NA   F[P]=NA
         R552P        Neutral    5        0.259   SNPs&GO

         T830S        Neutral    4        0.299   PhD-SNP:  F[T]=60%  F[S]=0%   Nali=4
         T830S   Unclassified   NA           NA   PANTHER:  F[T]=NA   F[S]=NA
         T830S        Neutral    9        0.045   SNPs&GO

        W1147L        Disease    6        0.804   PhD-SNP:  F[W]=100% F[L]=0%   Nali=95
        W1147L        Neutral    7        0.139   PANTHER:  F[W]=10%  F[L]=4%  
        W1147L        Neutral    4        0.321   SNPs&GO

        D1359E        Disease    6        0.811   PhD-SNP:  F[D]=91%  F[E]=0%   Nali=10
        D1359E        Neutral    7        0.145   PANTHER:  F[D]=19%  F[E]=8%  
        D1359E        Neutral    5        0.239   SNPs&GO

        R2321T        Neutral    6        0.212   PhD-SNP:  F[R]=50%  F[T]=0%   Nali=21
        R2321T        Neutral    6        0.209   PANTHER:  F[R]=23%  F[T]=4%  
        R2321T        Neutral    9        0.040   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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