Library Guides: Bioinformatics: Medical genetics

Medical genetics resources

Broad Institute
Freely available data, software and tools for genomic analysis (archived link page; some links may no longer work).
California Biobank Program
The California Biobank Program (CBP) represents the combined biospecimen and data resources of two California Department of Public Health (CDPH) screening and monitoring programs, the California Birth Defects Monitoring Program (CBDMP) and the California Genetic Disease Screening Program (GDSP). GDSP administers both the Newborn Screening Program (NBS) and the Prenatal Screening Program (PNS).
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The CBP has been mandated to make specimens and data available to researchers to identify risk factors for children's and women's diseases, develop and evaluate screening tests, develop and evaluate screening strategies, and develop and evaluate treatments.
DDBJ (DNA Data Bank of Japan)
A public database of annotated nucleotide sequences. Includes the Japanese Genotype-phenotype Archive (JGA), personal genotype and phenotype data from individuals who have signed consent agreements authorizing data release only for specific research uses.
ELIXIR
ELIXIR (The European Life-Science Infrastructure for Biological Information Resources) is an intergovernmental organization that provides a single integrated infrastructure for bioinformatics data, software tools, and training materials.
EMBL-EBI (European Bioinformatics Institute)
A collection of freely available tools and data resources including AlphaFold (protein structures), BioModels (computational models), ChEMBL (bioactive compounds), Ensembl (genome browser), Expression Atlas (gene expression), GWAS Catalog (genome-wide association studies), Protein Data Bank (3D structures), and UniProt (protein sequences).
ExPASy
Portal of the SIB Swiss Institute of Bioinformatics to databases and software tools in proteomics, genomics, phylogeny, systems biology, evolution, population genetics, and transcriptomics. Formerly the Expert Protein Analysis System.
GDC (Genomic Data Commons of the National Cancer Institute)
NCI-generated data from cancer genomic datasets, including The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Therapies (TARGET), supporting the elucidation of the molecular basis of cancer.
KEGG (Kyoto Encyclopedia of Genes and Genomes)
Resource for the integration and interpretation of large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
miRBase
A database of published miRNA sequences and annotations for hundreds of different species.
NCBI (National Center for Biotechnology Information)
Includes Clinically Relevant Variants (ClinVar), Database of Genotypes and Phenotypes (dbGaP), Database of Human Genetic Variation (dbVar), Gene Expression Omnibus (GEO), Genetic Testing Registry (GTR), MedGen, Online Mendelian Inheritance in Man (OMIM), and Single Nucleotide Polymorphisms (SNP).
NCBI Guide

Proteome This link opens in a new window
Protein information for species including human, mouse, rat, yeast, worm, and plant, including links to relevant scientific literature. Human entries include associated disease information.
PubMed This link opens in a new window
Citations and abstracts in the fields of biomedicine and health, as well as portions of the life sciences, behavioral sciences, chemical sciences, and bioengineering.

PubMed includes MEDLINE, PubMed Central (PMC), other biomedical and life science journals, and the NCBI Bookshelf. PubMed also provides links to other NCBI molecular biology resources, including nucleotide sequences, protein sequences, 3-D protein structure data, population study data sets, and assemblies of complete genomes in an integrated system.
Note: The link above goes to a specially configured version of PubMed for UC Berkeley users that will display the Get It at UC button for full text article access. To use the free public version, please click here.

VectorBase
Provides genomic, phenotypic and population-centric data for invertebrate vectors of human pathogens. Sponsored by NIAID-BRC (National Institute of Allergy and Infectious Diseases Bioinformatics Resource Center).
UCSC Xena
Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables. The next generation of the UCSC Cancer Genomics Browser.

For resources on model organisms, please see Species-specific resources.

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Bioinformatics: Medical genetics

Medical genetics resources