Center for Human and Clinical Genetics
Leiden University Medical Center
Genetic variation databases
primer design software
- Pira-PCR - PCR Primer design for restriction analysis of single nucleotide polymorphisms
- Primo SNP - Tool for
designing sequence primers and evaluating RNA splicing effects
- SNPCheck3 - SNPCheck is a tool for performing checks for the presence of SNPs in predicted PCR primer binding sites. Subscription is necessary for batch checks.
SNP detection and effect
- GenEpi Toolbox- tools for the evaluation and prediction
of genetic-epidemiological data including human SNPs
- pfSNP- Potentially functional SNP Search Engine
- PolyPhen-2- prediction
of functional effects of human nsSNPs
- PupaSuite - an
interactive web-based SNP analysis tool that allows for the selection of
relevant SNPs within a gene
evaluating effects of single amino acid substitutions on protein function.
A tool to map human DNA variation onto proteins.
Copy number variation databases
Sequence variation nomenclature
- HGVS guidelines - Sequence variation nomenclature guidelines
of the Human Genome Variation Society
- Mutalyzer - a tool to check sequence variation descriptions
SNP Discovery tools
- novoSNP is a
program that will help you find variations (SNPs and short INDELs) in
- de novo indel detection and SNP identification in the context of high-throughput medical sequencing.
- PolyPhred -
a program that compares fluorescence-based sequences across traces obtained
from different individuals to identify heterozygous sites for single
- a polymorphism detection tool that detects homozygous SNPs and indels by
aligning shotgun reads to the finished genome sequence.
- SomaticSniper – WashU somatic SNV detection algorithm for whole genome resequencing data.
- VarScan – Somatic and germline variant detection for massively parallel sequencing
If you have any comments or suggestions be sure to let me know!
Last modified: December 17, 2013