Molecular Pathology Laboratory
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The complete guide for available proteomic and genomic databases


Locus Reference Genomic

EVS Washington
Exome Assistant

Exome Pathways KGG


Genome TV

Locus specific Database 1 (UMD)
Locus specific Database 2 (BIC)
Locus specific Database 3 (Insight-group)

Ligand protein binding database (BioLip)
Prediction of protein function from 3D structure (ProFunc)


1000 Genomes

Catalogue of Somatic Mutation in Cancer (COSMIC)

 Encyclopedia of DNA Elements (ENCODE)

Geuvadis RNA sequencing project of 1000 Genomes samples

Mouse Genome Informatics (MGI)

Singel Nucleotide Polymorphism (SNP) Databases 

SNP detection and effect prediction

  • 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
  • SIFT PROVEAN-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
  • SNAP- evaluating effects of single amino acid substitutions on protein function.
  • snp2prot- A tool to map human DNA variation onto proteins.

Copy number variation databases

Disease-causing variations

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 resequencing projects.
  • PolyScan - 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 nucleotide substitutions.
  • ssahaSNP - 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

SNP-specific 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.



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