Resources - Databases

Databases & Data

Genomics and Sequence Databases

• GenBank
  Repository for nucleotide sequences and their protein translations. Includes annotations and metadata.

• Ensembl Genome Browser
  Genome-scale data for vertebrates, plants, and more. Includes annotations, comparative genomics, and regulatory data.

• UCSC Genome Browser
  Interactive platform for viewing genome assemblies with data on genes, sequences, regulatory elements, and conservation.

• RefSeq
  Curated collection of DNA, RNA, and protein sequences. Provides reference standards for genome annotation.

• DDBJ (DNA Data Bank of Japan)
  Partner to GenBank and EMBL-EBI, sharing nucleotide sequence data globally.

• GATK Resource Bundle
  A comprehensive set of reference files, including:

  • Human reference genomes (e.g., GRCh38, hg19)
    
  • Variant calling reference files like known SNPs (dbSNP) and indels (Mills_and_1000G).
    
  • Precomputed files for Base Quality Score Recalibration (BQSR) and Variant Quality Score Recalibration (VQSR).

• dbSNP
  SNP reference files for population genetics and variant calling.

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Protein and Structural Databases

• UniProt
  Comprehensive resource for protein sequence and functional information.

• Protein Data Bank (PDB)
  Repository of 3D structural data of proteins, nucleic acids, and complexes.

• InterPro
  Functional analysis of proteins by classifying sequences into families.

• Pfam
  Database of protein families and associated annotations.

• STRING
  Database for protein-protein interaction networks.

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Functional and Pathway Databases

• KEGG (Kyoto Encyclopedia of Genes and Genomes)
  Collection of manually curated pathway maps and functional annotations.

• Reactome
  Curated pathways of biological processes.

• BioCyc
  Database of metabolic pathways and genome annotations.

• WikiPathways
  Open-access platform for biological pathway knowledge.

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Oncology and Cancer Genomics Databases

• COSMIC (Catalogue of Somatic Mutations in Cancer)
  Comprehensive database of somatic mutations in human cancers. Includes data on mutations, gene fusions, copy-number changes, and clinical correlations.

• GDC (Genomic Data Commons)
  Repository for cancer genomic and clinical data.

• ICGC (International Cancer Genome Consortium)
  Platform providing genomic and clinical data from cancer research studies.

• TCGA (The Cancer Genome Atlas)
  A dataset for cancer genomics and phenotypes.

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Microbial and Metagenomics Databases

• MG-RAST
  Platform for analysis of metagenomic data.

• Greengenes
  16S rRNA gene database for microbial taxonomy and phylogeny.

• SILVA
  Comprehensive database for ribosomal RNA sequences.

• IMG/M
  Integrated Microbial Genomes and Microbiomes platform.

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Epigenomics and Regulatory Databases

• ENCODE
  Resource of functional genomics data for gene regulation.

• Roadmap Epigenomics
  Epigenetic data for diverse cell types and tissues.

• JASPAR
  Open-access database of transcription factor binding profiles.

• GTRD (Gene Transcription Regulation Database)
  Transcription factor binding sites and gene regulation data.

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Metagenomics Tools

• QIIME2
  Platform for analysing and visualising microbiome data.

• Kraken2
  A taxonomic sequence classification system.

• MetaPhlAn
  A tool for profiling the composition of microbial communities.

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Variation and Population Genetics Databases

• 1000 Genomes Project
  Catalog of human genetic variation.

• gnomAD
  Aggregated human genome and exome data.

• HapMap
  Resource for human haplotypes and SNP frequencies.

• ExAC
  Database of exome sequencing data from diverse populations.

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Miscellaneous Resources

• Gene Ontology (GO)
  Resource for functional annotation of genes.

• ArrayExpress
  Archive for functional genomics data.

• BioSamples
  Metadata repository for biological samples.

• Human Protein Atlas
  Comprehensive data on protein expression in human tissues and organs.

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