| title | description | published | date | tags | editor | dateCreated |
|---|---|---|---|---|---|---|
Databases |
Here you will found the link to the wiki's pages of databases |
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2023-12-16 19:46:33 UTC |
category |
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2020-04-29 20:55:11 UTC |
- 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 {.links-list}
- 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 {.links-list}
- ⭐ 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 {.links-list}
- 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 {.links-list}
- 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) {.links-list}
- ⭐ 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 {.links-list}
- 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 {.links-list}
- 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 {.links-list}
- ⭐ 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 {.links-list}
- ⭐ 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 {.links-list}
- ModelSEED Resource for the reconstruction, exploration, comparison, and analysis of metabolic models {.links-list}
- ⭐ 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 {.links-list}
- 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 {.links-list}
- ⭐ 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 {.links-list}
- ⭐ 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 {.links-list}
- 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 {.links-list}
- ⭐ 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 {.links-list}