Gene ontology anotation alignment

 

Transcription proteomics

Sequencing portals

These tools or the interfaces have been developed by the GenomeNet, except the core programs for the sequence analysis.

Sequence analysis

Human cell
Human

Genome analysis

Gentaur Bioinformatics Center

University Bioinformatics Center. They are maintained by the individual laboratories.

1000 Genomes A Deep Catalog of Human Genetic Variation
2ZIP leucine zipper prediction server
A list of journals related to genetics and genomics, highlighting those that enforce the use of approved nomenclature.
AgBase a curated, open-source resource for functional analysis of agricultural plant and animal gene products
Amborella Genome Database
ANISEED Ascidian Network for InSitu Expression and Embryological Data
AnolisGenome a community resource site for Anolis genomics and genetic studies
Ant Genomes Portal
antiCODE database of non-redundant natural sense-antisense transcript pairs
AphidBase an aphid genomics database
ARKdb species databases includes: Cat, Chicken, Cow, Deer, Horse, Pig, Salmon, Sheep, Tilapia, Turkey
AspGD Aspergillus Genome Database
Atlas of Genetics and Cytogenetics in Oncology and Haematology
Avianbase a community resource for bird genomics
BeeBase
BeetleBase the model organism database for Tribolium castaneum
BioGPS Gene Portal System
Bioinformatics Analysis Tools
Bioinformatics Services at EMBL Heidelberg
Bioinformatics Services at EMBL-EBI
BirdBase A Database of Avian Genes and Genomes
Bolbase a comprehensive genomics database for Brassica oleracea
BouillaBase.org comparative genomics of cichlid fishes
BRAD Brassica Database
Brassica.info Sharing information worldwide for the Multinational Brassica Genome Project
BRENDA the Comprehensive Enzyme Information System
BUSCO Benchmarking Universal Single-Copy Orthologs
Cacao Genome Database
Caenorhabditis Genome Sequencing Projects
Candida Genome Database
CATH protein structure classification
cBARBEL – Catfish Genome Database
Chicken Genome Resources
Chinese Hamster Genome Database
ChlamydDB database for the green alga Chlamydomonas reinhardtii and related species
Citrus Genome Database
CoGe comparative genomics resource
COILS prediction of coiled coil regions in proteins
CORUM Comprehensive Resource of Mammalian protein complexes
COSMIC Catalogue of Somatic Mutations in Cancer
Cottongen Cotton Database Resources
CrocBase the crocodilian genomes project
Database of Genomic Variants
dbVar Database of Genomic Structural Variation
DDBJ DNA DataBank of Japan
DECIPHER
dictyBase central resource for Dictyostelid genomics
DIOPT DRSC Integrative Ortholog Prediction Tool
EBI Toolbox
EcoGene the Database of Escherichia coli Sequence and Function
Education Resources
EggNog evolutionary genealogy of genes: Non-supervised Orthologous Groups
ENA European Nucleotide Archive
ENCODE Project ENCyclopedia Of DNA Elements
Ensembl Genomes
Ensembl Human human genes generated automatically by the Ensembl gene builder
Ensembl genome databases for vertebrates and other eukaryotic species
EnsemblCompara
Entrez Gene searchable database of genes, defined by sequence and/or located in the NCBI Map Viewer
Enzyme Portal Your portal to enzyme-related information at the EBI
EuPathDB Eukaryotic Pathogen Database Resources
Europe PMC an archive of life sciences journal literature
European Nucleotide Archive (ENA) Advanced Search
Evola Evolutionary annotation database
ExPasy Proteomics tools
ExPASy Proteomics Server
ExplorEnz the Enzyme Database
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
GENATLAS database of human genes
Gene Wiki dedicated to the goal of applying community intelligence to the annotation of gene and protein function
Gene3D structural and functional annotation of protein families
GeneCards database of human genes
General gene and nucleic acid resources
GeneReviews expert-authored, peer-reviewed disease descriptions
GeneReviews peer-reviewed disease descriptions
GeneTests a medical genetics information resource developed for physicians, genetic counselors, other healthcare providers, and researchers
GeneTests disease profile database
Genetic Testing Registry a central location for voluntary submission of genetic test information by providers
Genetic Testing Registry disease profile database
Genome Databases and Browsers
Genome Reference Consortium Putting sequences into a chromosome context
GenomeNet Bioinformatics Tools
GenomeNet Database Resources
Genomic tRNA database contains tRNA gene predictions made by tRNAscan-SE
Genomicus Genomes in evolution
GHR Genetics Home Reference
GO Gene Ontology controlled vocabulary
Goat Genome Project
GOBASE the Organelle Genome Database
GOLD Genomes Online Database
Gramene a resource for comparative grass genomics
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
HCOP HGNC Comparison of Orthology Predictions
Heliconius Genome Project
HGD Hymenoptera Genome Database
HGMD Human Gene Mutation Database
HGVS database list Human Genome Variation Society
HieranoiDB
H-Invitational Database an integrated database of human genes and transcripts
HomoloGene
Horse Genome Project
HPRD the Human Protein Reference Database
HUGE database of Human Unidentified Gene-Encoded large proteins
Human Genome Databases, Browsers and Variation Resources
Human Genome Segmental Duplication Database
Human Genome Variation Society
Human Genome Variation Society Sequence Variant Nomenclature Guidelines
Human Phenotype Ontology
Human Proteinpedia a community portal for sharing and integration of human protein data
Human Structural Variation Database
Human Variome Project
HUPO Human Proteome Organisation
IECA International E.coli Alliance E.coli Database Portal
IMG integrated microbial genomes and metagenomes
IMGT/GENE-DB the international ImMunoGeneTics information system for immunoglobulins
InParanoid eukaryotic ortholog groups
INSDC International Nucleotide Sequence Database Collaboration
InterPro database of protein families, domains and functional sites
InterProScan scans sequences for a range of protein signatures
IsoBase A Database of Functionally Related Orthologs
IUBMB International Union of Biochemistry and Molecular Biology
IUPHAR the International Union of Basic and Clinical Pharmacology
JGI Genome Portal
Journals
KEGG Kyoto Encyclopedia of Genes and Genomes
KO KEGG Orthology Database
Leiden Locus Specific Database list
List of public Leiden Open Variant Database (LOVD) installations
lncRNAdb provides comprehensive annotations of eukaryotic long non-coding RNAs (lncRNAs)
LRRfinder – identifies leucine-rich repeats in protein sequences
Lyons Feline & Comparative Genetics
MaizeGDB Maize Genetics and Genomics Database
Mamit-tRNAdb compilation of mammalian mitochondrial tRNA genes
MEROPS a peptidase database
metaPhOrs
Metazome database and graphical user interface enabling comparative genomic studies within the metazoa
MGI Mouse Genome Informatics
MicrobesOnline
miRBase microRNA database
Mutalyzer sequence variant nomenclature checker
NasoniaBase
National Animal Genome Research Program
NATsDB repository of natural antisense transcripts (NATs)
NCBI BLAST
NCBI GenBank
NCBI Gene searchable database of genes, from RefSeq genomes, defined by sequence and/or located in the NCBI Map Viewer
NCBI Protein database
NCBI tools for data mining includes links to splign, ORF Finder, BLink, CD Search and much more
NC-IUPHAR International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification
ncRNA Expression Database (NRED) database of expression data on human and mouse long ncRNAs
Neuropeptides
Non-coding RNA Database
Non-Vertebrate Genome Databases and Browsers
OMA (Orthologous Matrix project)
OMIA Online Mendelian Inheritance In Animals
OMIM Online Mendelian Inheritance in Man
OpossumBase The Monodelphis domestica Genomic Resources Database
OPTIC Clade genomics web server
Orphanet the portal for rare diseases
OrthoDB The Hierarchical Catalog of Eukaryotic Orthologs
OrthoInspector
Orthology and Comparative Genomics Resources
OrthoMCL Ortholog Groups of Protein Sequences
Oryzabase Integrated Rice Science Database
Other gene and nucleic acid resources
Other Resources
Other Vertebrate Genome Databases and Browsers
OXGRID the Oxford Grid project
Panther Classification System
ParameciumDB a database for the model organism Paramecium tetraurelia
PATRIC Pathosystems Resource Integration Center
PDB Protein Data Bank
Pfam sequence search scans sequences against Pfam protein families
Pfam protein families database of alignments and HMMs
PHOG PhyloFacts Orthology Group
PhosphoSitePlus A protein modification resource
PhylomeDB
Pig Genome Coordination Program
Pig Genome Resources
PIR Protein Information Resource
piRNABank web resource on classified and clustered piRNAs
PlantGDB Tools and resources for plant genomics
PMDB Protein Model Database
PomBase a scientific resource for fission yeast
P-POD Princeton Protein Orthology Database
PROSITE database of protein domains, families and functional sites
Protein resources
Pseudogene.org genome analysis
Pseudomonas Genome Database
Pubmed more than 20 million citations for biomedical literature
Quest for Orthologs
QuickGO EMBL-EBI Gene Ontology browser
Rabbit Genome Resources
RAP-DB The Rice Annotation Project Database
Reactome knowledgebase of biological processes
RepBase database of repetitive DNA elements
RepeatMasker screens DNA sequences for interspersed repeats and low complexity DNA sequences
Rfam RNA families database of alignments and CMs
RGD Rat Genome Database
RhesusBase a knowledgebase for the monkey research community
Rice Genome Annotation Project
RIKEN GSC databases
RNAcentral resource to organise data for non-protein coding RNA genes
RNA-specific resources
SchistoDB Schistosoma Genomic Resources
SCOP Structural Classification of Proteins
SGD Saccharomyces Genome Database
SGN sol genomics network
SilkDB Silkworm Genome Database
SMART Simple Modular Architecture Research Tool
Sno/scaRNAbase curated repository for small nucleolar RNAs and small cajal body-specific RNAs
snoRNABase comprehensive database of human H/ACA and C/D box snoRNAs
SOSUI – transmembrane prediction server
SoyBase and the Soybean Breeder’s toolbox
SpBase Strongylocentrotus purpuratus Sea Urchin Genome Database
Splign utility for converting cDNA to genomic, or spliced sequence alignments
StellaBase Nematostella vectensis Genomics Database
Superfamily HMM library and genome assignments server
Superfamily HMM library and genome assignments server
SWISS-PROT ENZYME
TAIR The Arabidopsis Information Resource
TarBase curated database of experimentally supported microRNA targets
Tetraodon Genome Browser
TGD Tetrahymena Genome Database Wiki
TGI the Gene Index Project
The Bovine Genome Database
The Dog Genome Project
The Fugu Informatics Network
Tiger Genome Project
TMHMM prediction of transmembrane helices in proteins
TRANSFAC (transcription factor database)
TreeFam Tree families database
TreeGenes
tRNAscan-SE
UCL Bioinformatics Unit
UCSC Genome Bioinformatics
UCSC Human Genome Browser Gateway
UCSD-Nature Signaling Gateway
UniGene unique human gene sequence collection
UniProt Reference proteomes
UniProt the universal protein resource
VectorBase invertebrate vectors of human pathogens
VEGA Human manual annotation of finished genome sequence
VEGA Vertebrate Genome Annotation containing manual annotation of vertebrate finished genome sequence
VISTA Tools for Comparative Genomics
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.
wFleaBase Daphnia Water Flea Genome Database
Wikigenes
WormBase the biology and genome of C. elegans
Xenbase a Xenopus web resource
ZFIN Zebrafish Information Network
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