Genome bioinformatic analysis of nonsynonymous SNPs

BMC Bioinformatics

Table 2 Prediction methods. Summary of computational methods mentioned in this analysis

Method	Predicts effect on Structure	Predicts effect on Function	Requires structural information	Method	Number of nSNPs with predictions	Availability
SIFT	Implicit	implicit	No	SequenceConservation	22728	[22]
LS-SNP	Yes	yes	No	Knowledge-based rules and support vector machine	11220	[24]
POLYPHEN	yes	yes	Yes	Sequence Profile and structural properties	4459	[27]
SDM	Yes	no	Yes	Structure based Substitution Table	5705	Available On request
Imutant	yes	no	Yes	Support vector machine	8879	[19]
env_score	Yes	no	Yes	Structure based Substitution Table	10625	Available On request
Crescendo	No	yes	Yes	Structure based Substitution Table	10625	Available On request
FUGUE	N/A	N/A	No	Sequence Substitution Profile	N/A	[39]
Modeller	N/A	N/A	Yes		N/A	[43]

ISSN: 1471-2105