- The web portal to the NIH genetic sequence database maintained by NCBI, also a part of the International Nucleotide Database Collaboration. Literature citation, release notes and an example record can be found in this page.

 - The web portal to EMBL nucleotide sequence database maintained by EBI, also a part of the International Nucleotide Database Collaboration. Various documentations such as release notes, database statistics, user guide, feature table definition and sample entry and FAQs are provided.

 - A data repository for omics data maintained by the Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), serving as a primary archive of genome sequencing data.

 - The Reference Sequence collection constructed by NCBI to provide a comprehensive, integrated, non-redundant set of DNA, RNA sequences and protein products. It provides a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies and comparative analyses.

 - An Organized View of the Transcriptome created by NCBI. Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus, together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.

 - The database of single nucleotide polymorphism maintained by NCBI.

 - The main web site for international protein sequence database which consists of the protein knowledgebase (UniProtKB), the sequence clusters (UniRef) and the sequence archive (UniParc).

 - The main repository of macromolecular structures maintained by the Research Collaboration for Structural Bioinformatics.

 - The macromolecular database maintained by NCBI.

 - The entry point for the EBI macromolecular structure database.

 - The biological magnetic resonance data bank maintained at University of Wisconsin-Madison.

 - The structural biology knowledgebase maintained by the Protien Structure Initiative.

 - The database of comparative protein structure models developed and maintained at University of California, San Francisco.

 - The database of Structure Classification of Proteins developed and maintained by Cambridge University.

 - The database of Calcification, Architecture, Topology and Homologous superfamily developed and maintained by University College, London.

 - A database of protein domains, families and functional sites, created and maintained by the Swiss Institute of Bioinformatics.

 - A database of protein fingerprints consisting of conserved motifs within a protein family, created and maintained by Manchester University, UK.

 - A database of multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins, created and maintained by the Fred Hutchinson Cancer Research Center, US.

 - A database of conserved protein domains created and maintained by the NCBI structure group.

 - A database of comprehensive set of protein domain families automatically generated from the SWISS-PROT and TrEMBL sequence databases, developed and maintained by the University Claude Bernard, France.

 - A database of protein families represented by multiple sequence alignments and hidden Markov models, constructed and maintained by the Sanger Institute, UK.

 - A web site for the the human protein atlas which shows expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry images, developed and maintained by Proteome Resource Center, Sweden.

 - A database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes.

 - The web server of the European eukaryotic genome resource developed by EBI and the Sanger Institute.

 - The genome browser website containing the reference sequence and working draft assemblies for a large collection of genomes at the University of California at Santa Cruz (UCSC), originally known as GoldenPath.

 - The The NCBI genomic map viewer for the visualization of completed and ongoing genome sequence.

 - The entry portal to various NCBI genomic biology tools and resources, including the Map Viewer, the Genome Project Database and the Plant Genomes Central, etc.

 - The NCBI genomic information table lists the general information of genomes for all species.

 - A comprehensive suite of programs and databases for comparative analysis of genomic sequences.

 - Genomes Online Database, a comprehensive information resource for complete and ongoing genome sequencing projects with flowcharts and tables of statistical data.

 - The international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

 - The Rat Genome Database at the Wisconsin University, to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research.

 - The Aferican clawed frog Xenopus laevis and Xenopus tropicalis biology and genomics resource.

 - The Zebrafish International Resource Center.

 - A comprehensive database of drosophila genes and genomes maintained by Indiana University.

 - The biology and genome resource of the Caenorhabditis elegans genome.

 - The Saccharomyces Genome database.

 - A tool for green plant comparative genomics, maintained by the Center for Integrative Genomics, Joint Genome Institute.

 - A curated open-source data resource for comparative genome analysis in the grasses including rice, maize, wheat, barley, sorghum etc, as well as other plants including arabidopsis, poplar and grape. Cross-species homology relationships can be found using information derived from genomic and EST sequencing, protein structure and function analysis, genetic and physical mapping, interpretation of biochemical pathways, gene and QTL localization and descriptions of phenotypic characters and mutations.

 - The Arabidopsis information resource maintained by Stanford University. It includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.

 - Araport is a one-stop-shop for Arabidopsis thaliana genomics. Araport offers gene and protein reports with orthology, expression, interactions and the latest annotation, plus analysis tools, community apps, and web services. Araport is 100% free and open-source. Registered members can save their analysis, publish science apps, and post announcements.

 - A genome browser for the commonly studied plant model organism Arabidopsis thaliana.

 - A rice knowledgebase for data integration through community-contributed modules, integrating data from remote resources through web APIs and featuring collaborative integration of rice data from multiple committed modules and low costs for database update and maintenance.

 - A comprehensive rice science database maintained by National Institute of Genetics, Japan. It contains genetic resource stock information, gene dictionary, chromosome maps, mutant images and fundamental knowledge of rice science.

 - The community database for biological information about the crop plant Zea mays ssp. mays, with genetic, genomic, sequence, gene product, functional characterization, literature reference.

 - Integrating Genetics and Molecular Biology for Soybean Researchers.

 - A collection of data resource of the Solanaceae species including tomoto, potato, peppper, eggplant, petunia, nicotiana.

 - The web portal for the International Cucurbit Genomics Initiative including melon, cucumber, watermelen, pumpkin, etc.

Ensembl Protists

The Protist Compara has been extended and now includes all 32 previously included genomes and 57 of the new imports, selected to ensure each species is covered by at least one genome. Representative sequences have been selected by date of submission to INSDC (i.e. earlier submissions have been preferentially included).

Ensembl 

Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Ensembl Fungi

26 new genomes now available in Ensembl Fungi

From release 28 forward, all fungal genomes whose sequence and annotation has been completed and submitted to the the International Nucleotide Sequence Database Collaboration (i.e. the ENA, GenBank and DDBJ databases) is available in Ensembl Fungi. The release now consists of a total of 589 genomes, of which 536 have been taken from the archives and 53 taken directly from other sources. The new genomes have been functionally annotated with InterPro entries and GO terms using InterProScan v55, and manually curated GO terms have been projected from Saccharomyces cerevisiae and Schizosaccharomyces pombe to 1:1 orthologues in other species.The Fungal Compara is now calculated across 339 species. This includes all previously included genomes and the new imports, selected to ensure each species is represented by at least one genome. Representative sequences have been selected by date of submission to the INSDC (the earliest sequences submitted have been preferentially included).

 - the Bacterial Bioinformatics Resource Center, an information system designed to support the biomedical research community’s work on bacterial infectious diseases via integration of vital pathogen information with rich data and analysis tools.

 - The bacterial genome database maintained at the Pasteur Institute.

 - The genome database for cyanobacteria developed by Kazusa Institute, Japan.

 - the main page of NCBI viral genome information resource.

 - Global Initiative on Sharing Avian Influenza Data.

 - A database for human and animal influenza virus.

 - NCBI Influenza Virus Resource with influenza genomic data and analysis tools.

 - This site provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa.

文章整理自Abc.bioinformatics

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