Bioinformatics Links Directory : Sequence Polymorphisms

Links to various sequence polymorphism databases and resources concerning SNPs, short deletion, and insertion polymorphisms.

ARTS - (Found July 2, 2008 )

ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels.
http://andromeda.gsf.de/arts

PolyDoms - (Found July 2, 2008 )

PolyDoms is a database that maps human coding SNPs onto protein domains in an effort prioritize candidate mutations and polymorphisms.
http://polydoms.cchmc.org/polydoms/

PolyPhred - (Found July 2, 2008 )

UNIX-based tool for sequence trace based genotyping; integrated with PhredPhrapConsed (see DNA -- Contig Assembly); free for non-commercial use.
http://droog.mbt.washington.edu/PolyPhred.html

PupaSuite - (Found July 2, 2008 )

PupaSuite is a SNP analysis tool that allows for the selection of relevant SNPs within a gene based on the characteristics of the SNP. PupaSuite also provides information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs. PupaSuite was created to join PupaSNP & PupasView.
http://pupasuite.bioinfo.cipf.es

PupasView - (Found July 2, 2008 )

PupasView takes a single gene identifier as input and reports SNPs that have the potential to affect phenotype. In addition to looking for potential amino acid changes, PupaSNP also searches for SNPs with the potential to affect proper transcription, such as those in intronexon boundaries, predicted transcription factor binding sites, and exonic splicing enhancers.
http://pupasview.bioinfo.ochoa.fib.es/

QuickSNP - (Found July 2, 2008 )

QuickSNP is a resource for the selection of tagSNPs in the human genome that includes a gene-centric selection module.
http://bioinformoodics.jhmi.edu/quickSNP.pl

rSNP_Guide - (Found July 2, 2008 )

a system of databases documenting the influence of mutations in regulatory gene regions
http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/

SIFT - (Found July 2, 2008 )

Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.
http://blocks.fhcrc.org/sift/SIFT.html

SNP Cutter - (Found July 2, 2008 )

SNP Cutter is a tool that automates PCR-RFLP assay design for SNP genotyping.
http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm

SNPserver - (Found July 2, 2008 )

SNPServer combines BLAST, cap3 and a SNP discovery module into a single pipeline for the discovery of SNPs in user submitted files or dynamically created assemblies.
http://hornbill.cspp.latrobe.edu.au/snpdiscovery.html