Table 1 Existing SNP annotation tools
Name | Description | Type+ | Species | External Resources Used |
|---|---|---|---|---|
SNPit [15] | Analyses the potential functional significance of SNPs derived from genome wide association studies. | W | Human | dbSNP, EntrezGene, UCSC Browser, HGMD, ECR Browser, Haplotter, SIFT |
SNP Function Portal [16] | Explores the functional implication of SNP alleles | WD | Human | dbSNP, UniSTS, NCBI ideogram, Entrez Gene, NCBI human genome assembly, HapMap II project |
Pupasuite [17] | SNP prioritization and characterisation | WD | Human Mouse Rat | Ensembl, Gene Ontology, OMIM |
SNPnexus [18] | Provides functional annotation for both novel and public SNPs | WD | Human | NCBI RefSeq, UCSC Known Genes, VEGA, AceView |
LS-SNP/PDB [19] | Annotates non-synonymous SNPs mapped to Protein Data Bank structures | WD | Human | UniProtKB, Genome Browser, dbSNP, PDB |
F-SNP [20] | Computationally predicts functional SNPs for disease association studies | WD | Human | PolyPhen, SIFT, SNPeffect, SNPs3D, LS-SNP, ESEfinder, RescueESE, ESRSearch, PESX, Ensembl, TFSearch, Consite, GoldenPath, Ensembl, KinasePhos, OGPET, Sulfinator, GoldenPath |
FANS [21] | Functional analysis of novel SNPs | WD | Human Mouse | NCBI, Ensembl, UCSC BLAT, Rescue-ESE Fas-ESS, SIFT |
SNPer [22] | Facilitates the retrieval and use of Human SNPs for high-throughput research purposes. | WD | Human | dbSNP, Goldenpath, LocusLink, GeneOntology, SWISS-PROT, OMIM, Unigene |
SNAP [23] | An integrated SNP annotation platform | W | Human | Ensembl, UCSC, Uniprot, UniProt, Pfam, DAS-CBS, MINT, BIND, KEGG, TreeFam |
SNPeffect [13] | Predicts the effect of non-synonymous SNPs on the molecular phenotype of proteins. | W | Human | Ensembl human databases |
SNPs3D [24] | Assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis. | W | Human | dbSNP, SWIIS-Prot, RefSeq, Bioscience, Gene Ontology, KEGG, BIND, OMIM, HGMD, Entrez Gene |