Table 1.

Table includes the comparisons of different previous SNP annotation systems.

System Name	Focus	Limitations	Data Integration Type	Evaluation Type
FastSNP [9]	Changing amino acids, transcription factor, splicing	No mediated scheme, use of minor allele frequency as validation	Uses web wrappers	Case study, looking at allele frequencies
F-SNP [10]	splicing, transcription, translation and post- translation	Not federated, limited number of SNPs included, no evaluation	Data warehouse	None
LS-SNP [11]	Nonsynonymous SNPs, Protein sequences and models, pathways	Pipeline, links out to other sources	Data warehouse, links to outside sources	Case study
MutDB [7]	Missense SNPs	No evaluation, no federated integration system	Data warehouse, MySQL	None
PolyDoms [6]	Nonsynonymous SNPs	Lack of analysis tools, doesn’t look at LD, no evaluation	Data warehouse, Oracle	None
PupaSuite [12]	Transcription factor binding, splicing, introns, exons, evolutionary, haplotypes	No federated data integration, no evaluation	Data warehouse	None
SNPs3D [13]	Nonsynonymous SNPs and protein function, uses support vector machine learning	Not federated data integration,	MySQL database	Case study
SNPSelector [14]	Allele frequency, genotyping data	LD, dbSNP annotation, regulatory, repeat status	Data warehouse, MySQL	None