A Comprehensive Guide to Databases in Bioinformatics

Explore the NCBI site hosted by NIH, learn to search across databases and access APIs to retrieve gene, mRNA, and protein data from GenBank and FASTA formats.

Retrieve and explore gene sequences from the NCBI database, including RefSeq, GenBank, FASTA formats, and mRNA and protein variants, using genomic context and sequence viewer.

Explore NCBI resources such as PubMed Central, PubMed, PubChem, and Blast; learn to access genome, gene, and protein databases and download fasta, gtf, and gff formats for bioinformatics research.

Explore the sequence read archive as an INSDC repository for raw high-throughput sequencing data and learn how geo stores gene expression data sets and profiles with query and download tools.

Explore the NCBI dbSNP database for human genetic variations. See Bookshelf for open access life science books and the CDD tools for domain annotation.

Explore UniProt, a comprehensive protein sequence database and central knowledge base, featuring Swiss-prot and Trembl sections, plus tools like blast, peptide search, ID mapping, sparql, and programmatic api access.

Explore the UniProt database to search for a protein, view the protein page, and retrieve its amino acid sequence, then download fasta data in multiple formats.

Explore the protein data bank (PDB), a dynamic repository of 3D structures for proteins and nucleic acids, with coordinates, methods, and literature, used for discovery, understanding function, and drug design.

Explore the PDB database with tools for deposit, search, visualize, and analyze, including Molestar 3D visualization, sequence annotation viewer, and genome view.

Learn to search and navigate the PDB database, refine results with advanced search options, view 3D structures, and download PDB, FASTA, and annotation data for proteins.

Explore key PDB databases, including PDB 101 for structure exploration, Worldwide PDB with validation and deposition tools, M data source for electron microscopy structures, and nucleic acid knowledge base.

Learn to perform pairwise structural alignment with the PDB tool, compare protein structures by IDs, adjust chains and algorithms, and interpret RMSD, identity, and export options.

Learn to run protein blast against PDB, identify similar proteins, and infer 3D structures for proteins whose structures are not yet available using homology modeling and threading.

Explore the Kyoto Encyclopedia of Genes and Genome (KEGG) as a pathway database, linking genomes, pathways, and molecular networks across 16 databases categorized by system, genomic, chemical, and health information.

Navigate the KEGG database to explore pathways, tools, and viewers—pathway viewer, bright viewer, and genome browser—along with KEGG objects and identifiers, the KEGG API, and KEGG FTP access.

Learn how to search the KEGG database to explore pathways, modules, orthology, genes, genomes, metagenomes, compounds, reactions, enzymes, networks, and drugs, with practical search techniques and results interpretation.

Discover KEGG databases, including the KEGG pathway database, KEGG modules and KEGG orthology, and navigate the brite hierarchy to study metabolism, disease, and drugs.

Explore the Kegg tools for functional annotation and pathway mapping, including Blast Koala, Ghost Koala, Kegg mapper, and CAS, with hands-on overview of sequence analysis and ortholog clustering.

Explore the Expasy bioinformatics resource portal by the Swiss Institute of Bioinformatics, offering parallel search across 160+ databases and tools for genomics, proteomics, structural biology, and more.

Explore Expasy gene and genome tools for retrieving and analyzing genomic data, focusing on Arraymap, chip-seq, Grunge, and the SSA motif analysis server.

Explore Expasy's protein and proteomes tools to retrieve and analyze protein data, including Swiss-model, String, Pro site, Parasite, and related resources like Click to Drag.

Explore Expasy evolution and phylogeny tools, including Swiss Tree's gold standard gene phylogenies, Ralphie, orthologous, and Next clad, to infer phylogenies, assign clades, and perform quality checks on viral sequences.

Explore Expasy’s structural biology tools, including Swiss Talk, Swiss Doc, Open Structure, and Swiss Similarity, to perform protein-ligand docking and ligand-based virtual screening.

Explore Expasy's system biology tools, including ria, Mara, and Cellosaurus, with expert knowledge bases, regulatory portals, and tutorials for enzyme annotation and cell line data.

Explore Expasy's text mining and machine learning tools for bioinformatics, with a hands-on focus on viromes and the MHC motif atlas to visualize and analyze variants.

Explore specialized databases in bioinformatics, curated data tailored to specific organisms, molecules, or processes. Learn how precision, deep annotation, comparative analysis, hypothesis testing, and community collaboration drive research.

Explore FlyBase, a Drosophila genetic resource offering search, download, and analysis tools for genes, proteins, pathways, and expression, plus the ID validator, batch download, sequence downloader, and image browser.

Explore the Galaxy database, a web-based, open-source platform for genomics and NGS data analysis, offering tools, workflows, data visualization, and collaborative sharing.

Explore EcoCyc, an encyclopedia of Escherichia coli genes and metabolism for strain K-12 MG1655, and navigate genome, pathways, transcriptional regulation, transporters, and omics tools.

Explore the rat genome database (RGD) as a central resource for rat genetic and genomic data, disease associations, phenotypes, pathways, chemical interactions, and cross-species comparisons with mouse and human.

Learn about the ribosomal database project, offering online data analysis, RNA-derived phylogenetic trees, and aligned RNA sequences for bacteria, archaea, and fungi, with current access issues.

Access the HIV sequence database, a comprehensive, richly annotated repository of HIV and SIV sequences, offering advanced search by accession, country, and subtype, plus genome browser and Nextstrain phylogenies.

Rfam is a comprehensive database of noncoding RNA families and structured RNA elements, providing multiple sequence alignments, consensus secondary structures, covariance models, and text, sequence, and API search access.

Explore Mirbase, the central repository of microRNA sequences and annotations, detailing miRNA families, genomic coordinates, and tissue expression across 271 species for bioinformatics research.

Master efficient data retrieval from bioinformatics databases by using simple queries and navigating interfaces like NCBI and Ensembl. Leverage templates, visualization, and external tools such as Blast and Cluster Omega.

Explore sequence, structure, gene expression, and functional annotation analyses using major bioinformatics databases, applying tools like blast, PDB, GEO, Ensembl, UCSC, STRING, and GO/KEGG for comparative and network insights.

Learn to troubleshoot common bioinformatics database queries by addressing syntax errors, missing data, performance issues, connectivity problems, and security restrictions.

Navigate a comprehensive survey of bioinformatics databases, from NCBI, PubMed, and SRA to UniProt, PDB, KEGG, Expasy, and specialized resources like FlyBase and miRBase, covering data retrieval strategies and troubleshooting.