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Databases

Databases

Locus Reference Genomic

EVS Washington
Exomiser
Exome Assistant
Exome Pathways KGG

Gliders

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)

UniProt
NextProt
ExPASy

1000 Genomes
Ensembl

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 

• ALFRED - The ALlele FREquency Database
• CGAP SNP index
• CHIP Bioinformatics Portal
• dbSNP <=> Refseq
• dbSNP - Database of Single Nucleotide Polymorphisms
• dbQSNP - A database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods.
• FESD II - Functional element SNP database
• Forensic SNP Information
• F-SNP - functional SNPs, specifically prioritized for disease association studies
• Gene Viewer - displays SNPs in mRNA sequences
• GeneSNPs
• Genome Variation Server - GVS137(hg19)
• GWAScentral - a genotype-phenotype association database(formerly HGVBASE)
• GWAS_NHGRI- a catalog of GWAS studies
• International HapMap Project
• Japanese SNP Database
• Mouse SNP query (MGI)
• The database of polymorphic miRNA-target interactions
• PhenCode - variants from locus-specific databases displayed in the UCSC genome browser
• PolymiRTS Polymorphism in microRNA Target Site - a database of naturally occurring DNA variations in predicted and experimentally identified microRNA (miRNA) target sites
• SeattleSeq Annotation 129 - Genome build hg18 variant annotation
• SeattleSeq Annotation 137 - Genome build hg19 variant annotation
• SeattleSNPs - a variation discovery resource
• SNAP - SNP annotation and Proxy Search
• SNPedia-awiki investigating human genetics
• SNP@WEB - a web-based catalog of databases and tools for SNP studies.
• SNP500Cancer Database -
• SNPper Retrieve known SNPs by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions.
• Tagger - tool for the selection and evaluation of tag SNPs from genotype data

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

• Database of Genomic Variants - A curated catalogue of large-scale variation in the human genome
• DECIPHER - DatabasE of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources
• ECARUCA - European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations
• Human Structural Variation Database - Copy number variation database (Eichler lab, 2004)
• The Chromosome Anomaly Collection - contains examples of unbalanced chromosome abnormalities (UBCAs) without phenotypic effect
• CNV Project - The Copy Number Variation (CNV) Project Data Index
• Structural Genome Variation Nature Genetics 39(7s)(2007) Supplement highlighting recent advances in human genomic variation

Disease-causing variations

• Sequence variation database list List of disease-causing 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 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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