Useful links

Genome Databases and Browsers

Human Genome Databases, Browsers and Variation Resources

• Database of Genomic Variants
• dbVar Database of Genomic Structural Variation
• ENCODE Project ENCyclopedia Of DNA Elements
• Ensembl Human human genes generated automatically by the Ensembl gene builder
• Entrez Gene searchable database of genes, defined by sequence and/or located in the NCBI Map Viewer
• Genome Reference Consortium Putting sequences into a chromosome context
• GWAS Catalog The NHGRI-EBI Catalog of published genome-wide association studies
• GWAS Central centralized compilation of summary level findings from genetic association studies
• HapMap international HapMap Project
• H-Invitational Database an integrated database of human genes and transcripts
• Human Genome Segmental Duplication Database
• Human Genome Variation Society Sequence Variant Nomenclature Guidelines
• Human Structural Variation Database
• 1000 Genomes A Deep Catalog of Human Genetic Variation
• UCSC Human Genome Browser Gateway
• VEGA Human manual annotation of finished genome sequence

Other Vertebrate Genome Databases and Browsers

• AgBase a curated, open-source resource for functional analysis of agricultural plant and animal gene products
• AnolisGenome a community resource site for Anolis genomics and genetic studies
• ARKdb species databases includes: Cat, Chicken, Cattle, Deer, Horse, Pig, Salmon, Sheep, Tilapia, Turkey
• Avianbase a community resource for bird genomics
• BirdBase A Database of Avian Genes and Genomes
• BouillaBase.org comparative genomics of cichlid fishes
• The Bovine Genome Database
• Lyons Feline & Comparative Genetics
• cBARBEL - Catfish Genome Database
• Chicken Genome Resources
• Chinese Hamster Genome Database
• CrocBase the crocodilian genomes project
• The Dog Genome Project
• Ensembl genome databases for vertebrates and other eukaryotic species
• NCBI Gene searchable database of genes, from RefSeq genomes, defined by sequence and/or located in the NCBI Map Viewer
• The Fugu Informatics Network
• Goat Genome Project
• Horse Genome Project
• MGI Mouse Genome Informatics
• National Animal Genome Research Program
• OpossumBase The Monodelphis domestica Genomic Resources Database
• Pig Genome Coordination Program
• Pig Genome Resources
• Rabbit Genome Resources
• RGD Rat Genome Database
• RhesusBase a knowledgebase for the monkey research community
• Tetraodon Genome Browser
• Tiger Genome Project
• UCSC Genome Bioinformatics
• VEGA Vertebrate Genome Annotation containing manual annotation of vertebrate finished genome sequence
• Xenbase a Xenopus web resource
• ZFIN Zebrafish Information Network

Non-Vertebrate Genome Databases and Browsers

• Amborella Genome Database
• ANISEED Ascidian Network for InSitu Expression and Embryological Data
• Ant Genomes Portal
• AphidBase an aphid genomics database
• AspGD Aspergillus Genome Database
• BeeBase
• BeetleBase the model organism database for Tribolium castaneum
• Bolbase a comprehensive genomics database for Brassica oleracea
• BRAD Brassica Database
• Brassica.info Sharing information worldwide for the Multinational Brassica Genome Project
• Cacao Genome Database
• Caenorhabditis Genome Sequencing Projects
• Candida Genome Database
• ChlamydDB database for the green alga Chlamydomonas reinhardtii and related species
• Citrus Genome Database
• Cottongen Cotton Database Resources
• dictyBase central resource for Dictyostelid genomics
• EcoGene the Database of Escherichia coli Sequence and Function
• Ensembl Genomes
• EuPathDB Eukaryotic Pathogen Database Resources
• EzGenome infomation about manually curated prokaryotic genome projects
• FlyBase a database of the Drosophila genome
• Fourmidable ant genomics database
• FungiDB fungal and oomycete genomics resources
• GDR Genome Database for Rosaceae
• GOBASE the Organelle Genome Database
• Gramene a resource for comparative grass genomics
• Heliconius Genome Project
• HGD Hymenoptera Genome Database
• IECA International E.coli Alliance E.coli Database Portal
• IMG integrated microbial genomes and metagenomes
• JGI Genome Portal
• MaizeGDB Maize Genetics and Genomics Database
• MicrobesOnline
• NasoniaBase
• Oryzabase Integrated Rice Science Database
• ParameciumDB a database for the model organism Paramecium tetraurelia
• PATRIC Pathosystems Resource Integration Center
• PlantGDB Tools and resources for plant genomics
• PomBase a scientific resource for fission yeast
• Pseudomonas Genome Database
• RAP-DB The Rice Annotation Project Database
• Rice Genome Annotation Project
• SchistoDB Schistosoma Genomic Resources
• SGD Saccharomyces Genome Database
• SGN sol genomics network
• SilkDB Silkworm Genome Database
• SoyBase and the Soybean Breeder’s toolbox
• SpBase Strongylocentrotus purpuratus Sea Urchin Genome Database
• StellaBase Nematostella vectensis Genomics Database
• TAIR The Arabidopsis Information Resource
• TGD Tetrahymena Genome Database Wiki
• TreeGenes
• VectorBase invertebrate vectors of human pathogens
• wFleaBase Daphnia Water Flea Genome Database
• WormBase the biology and genome of C. elegans

Orthology and Comparative Genomics Resources

• BUSCO Benchmarking Universal Single-Copy Orthologs
• CoGe comparative genomics resource
• DIOPT DRSC Integrative Ortholog Prediction Tool
• EggNog evolutionary genealogy of genes: Non-supervised Orthologous Groups
• EnsemblCompara
• Evola Evolutionary annotation database
• Genomicus Genomes in evolution
• HCOP HGNC Comparison of Orthology Predictions
• HieranoiDB
• HomoloGene
• InParanoid eukaryotic ortholog groups
• IsoBase A Database of Functionally Related Orthologs
• KO KEGG Orthology Database
• metaPhOrs
• Metazome database and graphical user interface enabling comparative genomic studies within the metazoa
• OMA (Orthologous Matrix project)
• OPTIC Clade genomics web server
• OrthoDB The Hierarchical Catalog of Eukaryotic Orthologs
• OrthoInspector
• OrthoMCL Ortholog Groups of Protein Sequences
• OXGRID the Oxford Grid project
• P-POD Princeton Protein Orthology Database
• Panther Classification System
• PHOG PhyloFacts Orthology Group
• PhylomeDB
• Quest for Orthologs
• TreeFam Tree families database
• UniProt Reference proteomes
• VISTA Tools for Comparative Genomics

Other gene and nucleic acid resources

General gene and nucleic acid resources

• BioGPS Gene Portal System
• COSMIC Catalogue of Somatic Mutations in Cancer
• DDBJ DNA DataBank of Japan
• DECIPHER
• ENA European Nucleotide Archive
• GENATLAS database of human genes
• Gene Wiki dedicated to the goal of applying community intelligence to the annotation of gene and protein function
• GeneCards database of human genes
• GeneReviews peer-reviewed disease descriptions
• GeneTests disease profile database
• Genetic Testing Registry disease profile database
• GenomeNet Database Resources
• GHR Genetics Home Reference
• HGMD Human Gene Mutation Database
• HGVS database list Human Genome Variation Society
• IMGT/GENE-DB the international ImMunoGeneTics information system for immunoglobulins
• INSDC International Nucleotide Sequence Database Collaboration
• KEGG Kyoto Encyclopedia of Genes and Genomes
• List of public Leiden Open Variant Database (LOVD) installations
• Leiden Locus Specific Database list
• NCBI GenBank
• OMIA Online Mendelian Inheritance In Animals
• OMIM Online Mendelian Inheritance in Man
• Pseudogene.org genome analysis
• RepBase database of repetitive DNA elements
• TGI the Gene Index Project
• UniGene unique human gene sequence collection
• Wikigenes

RNA-specific resources

• antiCODE database of non-redundant natural sense-antisense transcript pairs
• Genomic tRNA database contains tRNA gene predictions made by tRNAscan-SE
• lncRNAdb provides comprehensive annotations of eukaryotic long non-coding RNAs (lncRNAs)
• Mamit-tRNAdb compilation of mammalian mitochondrial tRNA genes
• miRBase microRNA database
• NATsDB repository of natural antisense transcripts (NATs)
• ncRNA Expression Database (NRED) database of expression data on human and mouse long ncRNAs
• Non-coding RNA Database
• piRNABank web resource on classified and clustered piRNAs
• Rfam RNA families database of alignments and CMs
• RNAcentral resource to organise data for non-protein coding RNA genes
• snoRNABase comprehensive database of human H/ACA and C/D box snoRNAs
• Sno/scaRNAbase curated repository for small nucleolar RNAs and small cajal body-specific RNAs
• TarBase curated database of experimentally supported microRNA targets

Protein resources

• BRENDA the Comprehensive Enzyme Information System
• CATH protein structure classification
• CORUM Comprehensive Resource of Mammalian protein complexes
• Enzyme Portal Your portal to enzyme-related information at the EBI
• ExPASy Proteomics Server
• ExplorEnz the Enzyme Database
• Gene3D structural and functional annotation of protein families
• HPRD the Human Protein Reference Database
• HUGE database of Human Unidentified Gene-Encoded large proteins
• Human Proteinpedia a community portal for sharing and integration of human protein data
• HUPO Human Proteome Organisation
• InterPro database of protein families, domains and functional sites
• IUPHAR the International Union of Basic and Clinical Pharmacology
• MEROPS a peptidase database
• NCBI Protein database
• Neuropeptides
• PDB Protein Data Bank
• Pfam protein families database of alignments and HMMs
• PhosphoSitePlus A protein modification resource
• PIR Protein Information Resource
• PMDB Protein Model Database
• SCOP Structural Classification of Proteins
• Superfamily HMM library and genome assignments server
• SWISS-PROT ENZYME
• TRANSFAC (transcription factor database)
• UniProt the universal protein resource

Bioinformatics Analysis Tools

• Bioinformatics Services at EMBL-EBI
• Bioinformatics Services at EMBL Heidelberg
• COILS prediction of coiled coil regions in proteins
• EBI Toolbox
• ExPasy Proteomics tools
• GenomeNet Bioinformatics Tools
• InterProScan scans sequences for a range of protein signatures
• LRRfinder - identifies leucine-rich repeats in protein sequences
• Mutalyzer sequence variant nomenclature checker
• NCBI BLAST
• NCBI tools for data mining includes links to splign, ORF Finder, BLink, CD Search and much more
• Pfam sequence search scans sequences against Pfam protein families
• PROSITE database of protein domains, families and functional sites
• RepeatMasker screens DNA sequences for interspersed repeats and low complexity DNA sequences
• SMART Simple Modular Architecture Research Tool
• SOSUI - transmembrane prediction server
• Splign utility for converting cDNA to genomic, or spliced sequence alignments
• Superfamily HMM library and genome assignments server
• TMHMM prediction of transmembrane helices in proteins
• tRNAscan-SE
• UCL Bioinformatics Unit
• 2ZIP leucine zipper prediction server

Journals

A list of journals related to genetics and genomics, highlighting those that enforce the use of approved nomenclature.

Education Resources

We have created a page to provide easy access to public engagement of science and related information on the Web and can be found here.

Other Resources

• Atlas of Genetics and Cytogenetics in Oncology and Haematology
• Europe PMC an archive of life sciences journal literature
• European Nucleotide Archive (ENA) Advanced Search
• GeneReviews expert-authored, peer-reviewed disease descriptions
• GeneTests a medical genetics information resource developed for physicians, genetic counselors, other healthcare providers, and researchers
• Genetic Testing Registry a central location for voluntary submission of genetic test information by providers
• GO Gene Ontology controlled vocabulary
• GOLD Genomes Online Database
• Human Genome Variation Society
• Human Phenotype Ontology
• Human Variome Project
• IUBMB International Union of Biochemistry and Molecular Biology
• NC-IUPHAR International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification
• Orphanet the portal for rare diseases
• Pubmed more than 20 million citations for biomedical literature
• QuickGO EMBL-EBI Gene Ontology browser
• Reactome knowledgebase of biological processes
• RIKEN GSC databases
• UCSD-Nature Signaling Gateway