¶ Databases
¶ Databases Related To Enzymes And Pathways
- cpnDB Manually curated, taxonomically broad collection of chaperonin sequences
- FuzDB Fuzzy protein complexes based on experimental evidence
- InnateDB Genes, proteins, interactions and signaling pathways involved in the innate immune response
- KEGG PATHWAY Manually drawn pathway maps representing our knowledge on molecular interaction
MetaCyc Curated database of experimentally elucidated metabolic pathways- Pathguide Provides an overview of more than 190 biological pathway and network databases
- PROSITE Database of protein families and domains
- SABIO-RK Curated database that contains information about biochemical reactions
- SimpleClinVar Web server to explore and retrieve gene and disease variants aggregated in ClinVar database
¶ Database Searches
- Batch-Entrez Entrez accession numbers or other identifiers, Batch Entrez downloads the corresponding records
- Bio.tools Comprehensive registry of software and databases
- ProDom Comprehensive set of protein domain families automatically generated from the UniProt KD
¶ Data Integration Databases
- BioCyc Collection of 16,822 Pathway/Genome Databases (PGDBs)
- BRENDA ENZYMES Main collection of enzyme functional data available
- CATH Classification of protein structures downloaded from the Protein Data Bank
- DEG Database of Essential Genes
- DisProt Database of intrinsically disordered proteins
- EuPathDB Eukaryotic pathogens database
- ExPASy ENZYME Repository of enzymes and information relative to the nomenclature of enzymes
- FungiDB Fungus database
- FungiPath Orthologous proteins in fungal genomes database
- GenomeNet Database Database of integrated genomes
- JGI GOLD Genomes Online Database
- PDBe-KB Community-driven resource managed by the PDBe team
- QuartataWeb User-friendly server developed for polypharmacological and chemogenomics analyses
- Reactome Signaling and metabolic molecules and their relations organized into biological pathways
- SCOP2 Description of the structural and evolutionary relationships between all proteins whose structure is known
- SCOPe Database developed at the Berkeley Lab and UC Berkeley
- SEED Viewer Allows users to access the latest curated datasets for comparative genomics
¶ General Databases
- cBiT Repository that offers biomaterial-based transcriptomics data together with biomaterial metadata
- Database Commons Provides users with access to a collection of publicly available biological databases
- DoriC A database of oriC regions in bacterial genomes
- ECOD Hierarchical classification of protein domains according to their evolutionary relationships
- InterPro Functional analysis of proteins by classifying them into families and predicting domains
- JGI Joint Genome Institute - Main webiste
- JGI Genome Portal JGI genomic databases and analytical tools
- KBase Large-scale bioinformatics system that enables users to upload their own data
- NCBI National Center for Biotechnology Information - Main website
- NPAtlas Designed to cover all microbially-derived natural products published
- RPFdb Public resource for hosting, analyzing and visualizing ribosome profiling (Ribo-seq) data
- UniProt Comprehensive resource for protein sequence and annotation data
¶ Eukaryote Databases
¶ Plant Databases
- Gramene Integrated data resource for comparative functional genomics in crops and model plant species
- JGI-Phytozome Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute
- PlantGDB Resources for comparative plant genomics
- PlantPromoterDB Provides comprehensive transcriptional regulatory elements informations
- PlnTFDB Identification and cataloging all Plant genes involved in transcriptional control
- Plprot Plastid protein database-integrates data from large scale proteome analyses
- The Plant Proteome DataBase Database for Arabidopsis thaliana and maize (Zea mays)
¶ Organism Specific Databases
- Arabidopsis Information Resource (TAIR) database of genetic and molecular biology data for A. thaliana
- ALGAEpath Coexpression Analysis on algae
- BioXpress Gene/miRNA expression in cancer database with expression levels mapped to genes or miRNAs
- BioMuta Single-nucleotide variation (SNV) in cancer and disease association database
- CellMap Storing and visualizing genetic interactions in S. cerevisiae
- ChlamyNet Clusters Exploration of gene co-expression network of Chlamydomonas transcriptome
- HumanMine An integrated database of Homo sapiens genomic data
- MaizeGDB Focused on the crop plant and model organism Zea mays
- neXtProt Exploring the universe of human proteins
- OncoMX Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data
- PomBase Scientific resource for fission yeast
- Saccharomyces Genome Database Comprehensive integrated biological information for the budding yeast S. cerevisiae
- SEEK Computational gene co-expression search engine
- SPELL Query-driven search engine for large gene expression microarray compendia on S. cerevisiae
¶ Prokaryote Databases
- ATGCs Resource for micro- and macro-evolutionary studies of Bacteria and Archaea
- JGI-IMG/Microbes Community resource for analysis and annotation of genome
- NCBI Microbial Database
¶ Bacterial Databases
- ASAP Relational database distributes genome sequence data and gene expression data
- BacMap An Interactive Atlas for Exploring Bacterial Genomes
- eLMSG Intended to integrate microbial systematics, genomics and phenomics
- OperonDB Predicting operons in microbial genomes
- PATRIC Data and analysis tools to support biomedical research on bacterial infectious diseases
- PRODORIC Integrated approach to provide information about molecular networks in prokaryotes
- PubSEED SEED is a constantly updated integration of genomic data
- xBASE Genome database aimed at helping laboratory-based bacteriologists
¶ Organism Specific Databases
- AureoWiki Repository of the Staphylococcus aureus research & annotation
- CyanoEXpress Curated genome-wide expression data for the cyanobacterium Synechocystis sp. PCC 6803
- EchoBASE Integrated post-genomic database for E.coli
- EcoCyc Scientific database for the bacterium Escherichia coli K-12 MG1655
- EcoliNet Probabilistic functional gene network for Escherichia coli
- PHIDIAS Data related to pathogen-host interactions for pathogens
- Pseudomonas Genome DB Genome annotation and genome analysis data of Pseudomonas
- SalCom HintonLab's Salmonella enterica serovar Typhimurium Gene Expression Compendium
- SToPSdb Sub-cellular Topology of Polypeptides in Streptomyces
- SubtiWiki Relational database of B. subtilis
- SynWiki Dedicated to the current generated functional annotation of the synthetic organism JCVI-syn3.0/syn3A
- TB Genomes Database An integrated platform for Tuberculosis research
¶ Archaeal Databases
¶ Virus Databases
- JGI-IMG/Virus Community resource for analysis and annotation of genome
- GiantVirus Mimivirus and other large DNA viruses
- RVDB Enhancing virus detection using next-generation sequencing (NGS) technologies
- PhagesDB Characterization, and genomics of phages that infect bacterial hosts within the phylum Actinobacteria
- PHASTER Rapid identification and annotation of prophage sequences within bacterial genomes and plasmids
- pVOGs Orthologous groups shared among complete genomes of viruses that infect bacteria and archaea
- ViPR Information for human pathogenic viruses
- VirusHostDB Linking virus genomes with host taxonomy
- VOGDB Virus orthologous groups
¶ Metabolic Pathways
- ModelSEED Resource for the reconstruction, exploration, comparison, and analysis of metabolic models
¶ Microarray and RNAseq Databases
- ATTED-II Coexpression database for plants to discover relationships of unknown genes within a species
- ArrayExpress Functional Genomics Data stores data from high-throughput functional genomics experiments
- Colombos Exploring and analyzing comprehensive organism-specific cross-platform expression of Bacteria
- COXPRESdb Database providing coexpression information for 11 animal species
- eFP Schematic representation of data for Arabidopsis seedlings
- GenExpDB Repository for E. coli gene expression data
- Harmonizome Comprehensive resource of knowledge about genes and proteins
- NCBI Gene Expression Omnibus (GEO)
- qTeller for MaizeGDB Comparative RNA-seq expression platform for Zea mays genome
- iModulon Expression and modulons for bacteria
¶ Ortholog Databases
- KEGG Ortholog Cluster Database of ortholog clusters (OCs) based on the whole genome comparison
- KofamKOALA Assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam
- MBGD Workbench system for comparative analysis of completely sequenced microbial genomes
- OrthoDB OrthoDB presents a catalog of orthologous protein-coding genes
- OrthoMCL OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences
- OrthoVenn2 Platform for comparison and annotation of orthologous gene clusters among multiple species
- WebNetCoffee Web server based on the algorithm of NetCoffee for aligning multiple PPI networks
¶ Phenotypes And Fitness Databases
- Chemgen Searching of growth data (strains/condition) of various E. coli
- CTD Advance understanding about how environmental exposures affect human health
- FitDB Searchable database of quantitative chemical-genetic interactions
- FitnessBrowser Browse thousands of genome-wide fitness experiments from diverse bacteria
- GenAtlas Scientific and clinical digests on genes and diseases
- GeneCards The Human Gene Database
- MorphoBank Database of peer-reviewed morphological matrices
- OGEE Aims to enhance our understanding of the essentiality of genes
- OMIM Comprehensive, authoritative compendium of human genes and genetic phenotypes
- VarSite Aims to annotate known disease-associated variants in human genes with structural information
¶ Post-Translational Modification Databases
¶ Protein-Protein Interaction Databases
- APID Agile Protein Interactomes DataServer gives a thorough collection of protein interactomes
- CellPhoneDB Repository of curated receptors, ligands and their interactions
- DIP Catalogs experimentally determined interactions between proteins
- ChiPPI Chimeric Protein-protein Interaction Server
- Emili Lab Database Emili Lab research findings accessed via public databases
- IntAct Open source database system and analysis tools for molecular interaction data
- PhosphoSitePlus Comprehensive information and tools for the study of protein post-translational modifications
- Stitch Database of known and predicted interactions between chemicals and proteins
- ComplexPortal Curated encyclopaedic resource of macromolecular complexes from a number of key model organisms
¶ Transcription Factor Databases
- CollecTF Database of transcription factor binding sites in the Bacteria domain
- RegPrecise database for capturing, visualization and analysis of transcription factor regulons
- RegulonDB Database on transcriptional regulation in Escherichia coli K-12 containing knowledge
¶ RNA Database
- 3dmodmap Database of maps showing the sites of modified rRNA nucleotides in 3D models
- GtRNAdb tRNA database contains tRNA gene predictions made by the program tRNAscan-SE
- Modomics Database of RNA modifications
- NONCODE Integrated knowledge database dedicated to non-coding RNAs (excluding tRNAs and rRNAs)
- scRNASeqDB Curated public single-cell gene expressing profiles for the wider research community
- The RNA Modification Database Listing of posttranscriptionally modified nucleosides from RNA
- T-Psi-C Allows you to search across all available tRNA sequences
- UCSC GtRNAdb tRNAscan-SE analysis of complete genomes
¶ Unknown Gene/Enzyme Databases
- ADOMETA Bioinformatics resource designed to predict genes for orphan metabolic activities
- ORENZA Accurate and up to date list of Enzyme Activities for which no sequences are available
- Orphan Enzyme Project Associate an amino-acid sequence with every known orphan enzyme