Software and Databases for SNP Research

A wide variety of tools and databases for SNP discovery, assay design, tagging, and functional analysis are available to the community. Here are links to some particularly useful resources.

SNP Discovery

Tools for detecting polymorphisms using sequence trace data.

SNP Databases

Central resources for genetic and genomic data.

Assay Design Tools

Tools for designing various kinds of SNP assays.

SNP Selection and Tagging

Several different approaches to selection of SNPs and haplotyping.

Functional Analysis of SNPs

Tools for finding and analyzing functional SNPs.

SNP Discovery Tools
Polybayes	A tool for SNP discovery in redundant DNA sequences.
SSAHA-SNP	A polymorphism detection tool that uses the SSAHA alignment algorithm.
Polyphred	A SNP discovery package built on phred, phrap, and consed tools.
NovoSNP	A graphical, Java-based program (PC/Mac/Linux) to identify SNPs and indels.

SNP Databases
HapMap	The site for the International HapMap Project includes project information and genotype data.
dbSNP	The dbSNP homepage is a portal to NCBI's SNP database.
UCSC	The UCSC Genome Browser Annotation Database.
JSNP	A database of Japanese single nucleotide polymorphisms.
TSC	The SNP Consortium - single nucleotide polymorphisms for biomedical research.
HGVbase	A database of human genome variants for genotype-phenotype association analyses.
IIPGA	The Innate Immunity PGA project has data for ~83 innate immunity genes .

Assay Design Resources
PerkinElmer	A SNP assay database for FP-TDI genotyping.
SNPbox	A modular software package for large-scale primer design.
Oligofaktory	A visual tool for interactive oligonucleotide design.
SNPicker	A graphical tool for primer picking in designing mutagenic endonuclease restriction assays .
ViewGene	A graphical tool for polymorphism visualization and characterization.
PolySearch	A web based system integrating PubMed, human genome data and primer design tools.

SNP Selection Tools
HaploView	Haplotype analysis and tag SNP selection.
PolyMAPr	Polymorphism database mining, annotation, and functional analysis.
SNPper	Retrieval and analysis of human SNPs.
FESTA	Fragmented Exhaustive Search for TAgSNPs.
SNPselector	Selecting SNPs for genetic association studies.

Functional Analysis of SNPs
JASPAR	A transcription factor binding profile database
ASD	The Alternative Splicing Database Project
ESEfinder	NCBI's tool for finding exonic splicing enhancers (ESEs)