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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
         R782Q        Neutral    5        0.239   PhD-SNP:  F[R]=30%  F[Q]=24%  Nali=117
         R782Q        Neutral    8        0.110   PANTHER:  F[R]=10%  F[Q]=18% 
         R782Q        Neutral    9        0.038   SNPs&GO

         V830A        Neutral    1        0.466   PhD-SNP:  F[V]=38%  F[A]=1%   Nali=114
         V830A        Neutral    3        0.358   PANTHER:  F[V]=29%  F[A]=3%  
         V830A        Neutral    6        0.204   SNPs&GO

        E1021K        Neutral    1        0.445   PhD-SNP:  F[E]=22%  F[K]=4%   Nali=117
        E1021K        Neutral    6        0.179   PANTHER:  F[E]=17%  F[K]=5%  
        E1021K        Neutral    7        0.150   SNPs&GO

        E1491D        Neutral    2        0.389   PhD-SNP:  F[E]=44%  F[D]=0%   Nali=35
        E1491D        Neutral    7        0.153   PANTHER:  F[E]=21%  F[D]=6%  
        E1491D        Neutral    8        0.106   SNPs&GO

        L1516I        Neutral    5        0.260   PhD-SNP:  F[L]=55%  F[I]=0%   Nali=21
        L1516I        Neutral    8        0.098   PANTHER:  F[L]=15%  F[I]=8%  
        L1516I        Neutral    9        0.039   SNPs&GO

        R1561T        Neutral    1        0.426   PhD-SNP:  F[R]=59%  F[T]=0%   Nali=31
        R1561T   Unclassified   NA           NA   PANTHER:  F[R]=NA   F[T]=NA
        R1561T        Neutral    8        0.109   SNPs&GO

        K1562N        Neutral    6        0.182   PhD-SNP:  F[K]=32%  F[N]=4%   Nali=27
        K1562N   Unclassified   NA           NA   PANTHER:  F[K]=NA   F[N]=NA
        K1562N        Neutral    9        0.060   SNPs&GO

        K1565N        Neutral    4        0.281   PhD-SNP:  F[K]=50%  F[N]=4%   Nali=25
        K1565N   Unclassified   NA           NA   PANTHER:  F[K]=NA   F[N]=NA
        K1565N        Neutral    8        0.088   SNPs&GO

        E1566D        Neutral    5        0.251   PhD-SNP:  F[E]=46%  F[D]=8%   Nali=25
        E1566D   Unclassified   NA           NA   PANTHER:  F[E]=NA   F[D]=NA
        E1566D        Neutral    8        0.110   SNPs&GO

        E1566Q        Neutral    7        0.162   PhD-SNP:  F[E]=46%  F[Q]=15%  Nali=25
        E1566Q   Unclassified   NA           NA   PANTHER:  F[E]=NA   F[Q]=NA
        E1566Q        Neutral    9        0.041   SNPs&GO

        K1567N        Neutral    1        0.446   PhD-SNP:  F[K]=58%  F[N]=0%   Nali=25
        K1567N   Unclassified   NA           NA   PANTHER:  F[K]=NA   F[N]=NA
        K1567N        Neutral    7        0.153   SNPs&GO

        A1569P        Disease    0        0.500   PhD-SNP:  F[A]=32%  F[P]=4%   Nali=24
        A1569P   Unclassified   NA           NA   PANTHER:  F[A]=NA   F[P]=NA
        A1569P        Neutral    7        0.163   SNPs&GO

        A1611T        Neutral    1        0.475   PhD-SNP:  F[A]=37%  F[T]=0%   Nali=42
        A1611T        Neutral    8        0.117   PANTHER:  F[A]=9%   F[T]=4%  
        A1611T        Neutral    8        0.086   SNPs&GO

        V1641A        Disease    6        0.809   PhD-SNP:  F[V]=95%  F[A]=0%   Nali=41
        V1641A        Neutral    9        0.067   PANTHER:  F[V]=9%   F[A]=8%  
        V1641A        Neutral    4        0.281   SNPs&GO

        Y1653S        Disease    8        0.894   PhD-SNP:  F[Y]=98%  F[S]=0%   Nali=41
        Y1653S        Neutral    8        0.112   PANTHER:  F[Y]=4%   F[S]=11% 
        Y1653S        Neutral    2        0.388   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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