SNPs&GO

SNPs&GO
Predicting disease associated variations using GO terms

Sequence File: FA5_HUMAN.seq
Alignment File: FA5_HUMAN.seq.blast
GO-terms File: FA5_HUMAN.seq.go
Output File: output.txt


Mutation	Prediction	RI	Probability	Method

D107H	Neutral	4	0.323	PhD-SNP: F[D]=12% F[H]=1% Nali=300
	Neutral	5	0.240	PANTHER: F[D]=28% F[H]=5%
	Neutral	4	0.312	SNPs&GO

I387T	Disease	7	0.852	PhD-SNP: F[I]=72% F[T]=2% Nali=253
	Neutral	4	0.296	PANTHER: F[I]=25% F[T]=3%
	Disease	7	0.835	SNPs&GO

C613R	Disease	3	0.658	PhD-SNP: F[C]=5% F[R]=0% Nali=266
	Disease	0	0.510	PANTHER: F[C]=32% F[R]=1%
	Disease	8	0.895	SNPs&GO

K858R	Neutral	8	0.119	PhD-SNP: F[K]=40% F[R]=27% Nali=14
	Neutral	9	0.068	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 terms

F[X]: Frequency of residue X in the sequence profile
Nali: Number of aligned sequences in the mutated site