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http://www.ensembl.org/

Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

Proper citation: Ensembl (RRID:SCR_002344) Copy   

•   Source: SciCrunch Registry

http://protists.ensembl.org

The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Protists, which houses protists species. Sponsors: EnsembProtists is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute.

Proper citation: Ensembl Protists (RRID:SCR_013154) Copy   

•   Source: SciCrunch Registry

http://fungi.ensembl.org/index.html

The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Fungi, which houses fungal species. Sponsors: EnsembFungi is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute.

Proper citation: Ensembl Fungi (RRID:SCR_008681) Copy   

•   Source: SciCrunch Registry

http://plants.ensembl.org/index.html

Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Plants, which houses plant species. Sponsors: EnsembPlants is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute.

Proper citation: Ensembl Plants (RRID:SCR_008680) Copy   

•   Source: SciCrunch Registry

http://bacteria.ensembl.org/index.html

The Ensembl Genomes project produces genome databases for important species from across the taxonomic range, using the Ensembl software system. Five sites are now available, one of which is Ensembl Bacteria, which houses bacterial species. All bacterial collections in Ensembl Bacteria have been updated with the latest data from ENA and UniProtKB. New genomes have been added to Escherichia/Shigella (3 additional genomes) and Staphylococcus (3 additional genomes). The mapping of array probes has been expanded to all genomes in the Escherichia/Shigella and Staphylococcus collections. Ensembl Bacteria also now features improved interfaces for selecting regions of circular molecules a new visualisation allowing the large scale comparison of multiple genomes. In multi-synteny view, users can select multiple genomes and observe the syntenic relationships between them. Sponsors: EnsembBacteria is a project run by EMBL - EBI to maintain annotation on selected genomes, based on the software developed in the Ensembl project developed jointly by the EBI and the Wellcome Trust Sanger Institute.

Proper citation: Ensembl Bacteria (RRID:SCR_008679) Copy   

•   Source: SciCrunch Registry

http://metazoa.ensembl.org/index.html

Ensembl Genomes project produces genome databases for important species from across taxonomic range, using Ensembl software system. Five sites are now available, one of which is Ensembl Metazoa, which houses metazoan species.

Proper citation: Ensembl Metazoa (RRID:SCR_000800) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/

Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.

Proper citation: European Bioinformatics Institute (RRID:SCR_004727) Copy   

•   Source: SciCrunch Registry

http://www.uniprot.org/uniparc/

Database that contains publicly available protein sequences with stable and unique identifiers (UPI) which are never removed, changed or reassigned. UniParc tracks sequence changes in the source databases and archives the history of all changes. Information other than protein sequence must be retrieved from the UniParc source databases using the database cross-references.

Proper citation: UniParc (RRID:SCR_005818) Copy   

•   Source: SciCrunch Registry

http://search.cpan.org/~cmungall/go-db-perl/

Software resource that extends the functionality of go-perl (on which it depends) with GO Database access functionality. go-db-perl comes bundled with various scripts and a shell command line interface that can be used as standalone tools. Installation is more involved than for go-perl; you will need a MySQL database plus the requisite DBI and DBD Perl modules. Full installation instructions are included in the download. go-db-perl is in use both to drive AmiGO and internally within Ensembl. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: go-db-perl (RRID:SCR_005721) Copy   

•   Source: SciCrunch Registry