SNP identification and annotation tools

This section collects together tools that help identifying and annotation of SNPs. In addition some of them can be used to map SNPs to genes.

Programs available

• CandiSNPer
• MutaGeneSys
• MutationTagger
• PolySearch
• Snap
• SCAN
• MedRefSNP
• Varietas
• WGAviewer

Description of programs

CandiSNPer

CandiSNPer is  a tool that determines the LD region around a significant SNP from a GWAS. It provides a list with functional annotation and LD values for the SNPs found in the LD region. This tool can be used to map SNPs to genes also. 

website: CandiSNPer

Download:

Reference: Schmitt, AO, Assmus J, Bortfeldt, RH, and Brockmann, GA. CandiSNPer: a web tool for the identification of candidate SNPs for causal variants. Bioinformatics 26 (7) 2009. doi:10.1093/bioinformatics/btq068

MutaGeneSys

According to Karchin et al. MutaGenesys is a tool that identifies inderect correlations between SNPs and mutations from OMIM. MutaGeneSys uses genome-wide genotype data to estimate disease susceptibility. Our system integrates three data sources: the International HapMap project, whole-genome marker correlation data and the Online Mendelian Inheritance in Man (OMIM) database. It accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete. 

website: MutaGeneSys

Download: MutaGeneSys_10202007.tar.gz

Reference: Julia Stoyanovich and Itsik Pe'er. MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data. Bioinformatics 2008 24(3):440-442; doi:10.1093/bioinformatics/btm587  

MutationTagger

MutationTagger is a rule- and regular expression-based approach that allows for the retrieval of protein point mutations from the whole PubMed database specifically for any given protein. 

Reference: Rainer Winnenburg, Conrad Plake and Michael Schroeder. Improved mutation tagging with gene identifiers applied to membrane protein stability prediction. BMC Bioinformatics 2009, 10(Suppl 8):S3.doi:10.1186/1471-2105-10-S8-S3

PolySearch

PolySearch is a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. 

website: PolySearch

Download:

Reference: Cheng D, Knox C, Young N, Stothard P, Damaraju S, Wishart DS. PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W399-405. doi: 10.1093/nar/gkn296.

Snap

Snap is a server designed to analyze single genes and relationships between genes basing on SNPs in human genome. Several public databases are integrated.

website: Snap

Download:

Reference: Li, S., Ma, L., Li, H., Vang, S., Hu, Y., Bolund, L., Wang, J. "Snap: an integrated SNP annotation platform." Nucleic Acids Res. 2007 Jan 1; vol: 35 (Database issue): D707-10. doi:10.1093/nar/gkl969

SCAN

In addition to other functions of this program, it can be used to seach related genes of SNP by giving the rs-code as an input. This way program provides info about chromosome number, position, alleles, gene, feature left and right neighbour genes.

website: SCAN

Download:

Reference:Gamazon, E.R., Zhang W., Konkashbaev A., Duan S., Kistner E., Nicolae D.L., Dolan, M.E., Cox, N.J. SCAN: SNP and copy number annotation. Bioinformatics Advance Access published on November 17, 2009, doi:10.1093/bioinformatics/btp644

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MedRefSNP

MedRefSNP database  provides integrated information about SNPs collected from the PubMed and OMIM databases. The RefSNP identifiers are automatically identified and are linked to various information sources such as the dbSNP, the HapMap database, the Entrez Gene database, the UCSC genome browser, the CGAP Pathway Searcher, and genetic association databases. And, each SNP is checked to determine whether the PolyDoms, SNPs3D or PolyPhen databases predicts that the SNP affects the phenotype of the protein encoded by the gene carrying the SNP. Also, neighboring SNPs showing strong linkage disequilibrium (LD) with published SNPs are included, using HapMap data

website: MedRefSNP

Download:

Reference: Rhee et al. MedRefSNP: a database of medically investigated SNPs. Hum.Mutat., 2009, 30, 3, E460-6. doi:10.1002/humu.20914

Varietas

Varietas is a web-based database portal that has been designed to aid researchers to easily retrieve information on a set of variations (eg. SNPs and CNVs), related genes and genomic elements in a batch like manner. As an input user can give variety of different features such as SNPs, genes, keywords or locations, or any combinations of them. These inputs are queried against VarietasDB that contain integrated data from various biological databases (including Ensembl, dbSNP, GAD, SNPedia). 

website: Varietas

Download:

Reference:  Paananen J et al. Varietas: a functional variation database portal. Database (Oxford). 2010 Jul 29;2010:baq016. Print 2010.  doi:10.1093/database/baq016

WGAviewer

WGAViewer is a free software tool that is designed to provide a user-friendly interface to annotate, visualize, and help interpret the full set of P values indicating evidence of association resulting from a Whole Genome Association (WGA) study. Current version offers six classes of annotation: 1. Chromosome view of WGA results, 2. Genic annotation of WGA results, 3. Annotation for SNPs, 4. Gene/SNP finding , 5. Evidence from multiple genome scans and 6. supporting/QC databases. 

website: WGAviewer

Download:

Reference:  Ge et al. WGAViewer: Software for Genomic Annotation of Whole Genome Association Studies. Genome Res. 2008 Apr;18(4):640-3. doi: 10.1101/gr.071571.107.

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Useful databases

• GAD (The Genomic Association Database)

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Review articles

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Other articles

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Useful Links

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