Bioinformatics Tools

Nucleic Acid (DNA/RNA) Databases

• GenBank (NCBI): Comprehensive nucleotide sequence database.
  https://www.ncbi.nlm.nih.gov/genbank/

• EMBL-EBI (European Molecular Biology Laboratory): European nucleotide sequence archive.
  https://www.ebi.ac.uk/ena

• DNA Data Bank of Japan (DDBJ): Nucleotide sequence database from Japan.
  https://www.ddbj.nig.ac.jp

• RefSeq: Curated reference sequences for genomes, transcripts, and proteins.
  https://www.ncbi.nlm.nih.gov/refseq/

• 1000 Genomes Project: Human genome variation data.
  https://www.internationalgenome.org

Protein and Structure Databases

• UniProt: Comprehensive resource for protein sequence and functional information.
  https://www.uniprot.org

• Protein Data Bank (PDB): 3D structures of proteins, DNA, and RNA.
  https://www.rcsb.org

• PROSITE: Protein domains, families, and functional sites database.
  https://prosite.expasy.org

• Pfam: Protein families database with alignments and HMMs.
  https://pfam.xfam.org

• Protein Information Resource (PIR): Protein sequence and classification databases.
  https://proteininformationresource.org

Functional and Pathway Databases

• KEGG (Kyoto Encyclopedia of Genes and Genomes): Genomic, chemical, and pathway data.
  https://www.genome.jp/kegg/

• TRANSFAC: Database of eukaryotic transcription factors and their binding sites.
  https://genexplain.com/transfac/

• JASPAR: Open-access database of transcription factor binding profiles.
  https://jaspar.genereg.net

Phenotype and Disease Databases

• OMIM (Online Mendelian Inheritance in Man): Human genes and genetic disorders.
  https://omim.org

• PHI-base: Pathogen-host interaction data.
  http://www.phi-base.org

• Human Gene Mutation Database (HGMD) - Public Version: Known gene lesions causing inherited diseases (free academic access).
  http://www.hgmd.cf.ac.uk/ac/index.php

Specialized and Model Organism Databases

• PomBase: Fission yeast Schizosaccharomyces pombe data.
  https://www.pombase.org

• TAIR (The Arabidopsis Information Resource): Arabidopsis thaliana genome and genetics.
  https://www.arabidopsis.org

• SubtiWiki: Bacillus subtilis integrated database.
  https://subtiwiki.uni-goettingen.de

• Saccharomyces Genome Database : comprehensive scientific resource dedicated to the molecular biology and genetics of the budding yeast Saccharomyces cerevisiae (baker's yeast).  

https://www.yeastgenome.org 

• WormBase: The authoritative database for C. elegans biology, genetics, genomics, and molecular data 

https://www.wormbase.org

• FlyBase: The central and most comprehensive database for Drosophila melanogaster 

http://flybase.org/

Metabolomics and Chemical Databases

• Human Metabolome Database (HMDB): Detailed info on human metabolites.
  https://hmdb.ca

• DrugBank: Drug and drug target database.
  https://go.drugbank.com

• PubChem: Chemical molecules and their activities.
  https://pubchem.ncbi.nlm.nih.gov

Cancer and Genomic Data Portals

• cBioPortal for Cancer Genomics: Interactive exploration of cancer genomics data.
  https://www.cbioportal.org

• The Cancer Genome Atlas (TCGA) Data Portal: Cancer genomic and clinical data.
  https://portal.gdc.cancer.gov

• Stemformatics: high quality curated gene expression data 

https://www.stemformatics.org/

Comprehensive Neuroscience Databases

• Allen Brain Atlas: High-resolution gene expression maps of the brain across species, including human and mouse.
  https://portal.brain-map.org

• NeuroMorpho.Org: Repository of digitally reconstructed neurons from multiple species, providing morphological data.
  http://neuromorpho.org

• NeuroVault: Repository for unthresholded statistical maps from MRI and PET studies, useful for meta-analyses.
  https://neurovault.org

• OpenNeuro: Open platform for sharing a wide variety of neuroscience datasets, primarily human MRI and electrophysiology data. Contains thousands of datasets with diverse modalities.
  https://openneuro.org

• SchizConnect: Virtual database for schizophrenia neuroimaging data including MRI and clinical assessments.
  http://schizconnect.org

Brain Imaging and Structural Atlases

• Human Connectome Project: Extensive human brain imaging data including structural and functional MRI.
  https://humanconnectome.org

• BrainSpan Atlas of the Developing Human Brain: Transcriptomic and imaging data across human brain development stages.
  http://www.brainspan.org

• Whole Brain Atlas: Structural MRI and PET images covering healthy and diseased states.
  http://www.med.harvard.edu/AANLIB/home.html

Electrophysiology and Cellular Databases

• Primate Cell Type Database: Intracellular recordings and 3D neuronal reconstructions from primates and humans.
  http://primatedatabase.com

• NeuroElectro: Database of electrophysiological properties of neurons across species and brain regions.
  http://neuroelectro.org

Neuroscience Database Collections and Guides

• Cold Spring Harbor Laboratory Neuroscience Databases Guide: Curated list of neuroscience-specific databases including Allen Brain Atlas, Brain Architecture Project, and BrainSpan.
  https://cshl.libguides.com/c.php?g=523983

Scientific Tools