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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

https://github.com/Ensembl

Public database that stores areas of genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. Different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). Effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run same analysis on your own data using Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to quality control process to flag suspect data. In human, they calculate linkage disequilibrium for each variant, by population.

Proper citation: Ensembl Variation (RRID:SCR_001630) Copy   

•   Source: SciCrunch Registry

http://www.ensembl.org/info/docs/tools/vep/index.html

Data analysis service to predict the functional consequences of known and unknown variants.

Proper citation: Variant Effect Predictor (RRID:SCR_007931) Copy   

•   Source: SciCrunch Registry

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

Database of genomes that are in the process of being annotated are provided as an early access site for users. Genomes are here when the initial BLAST analysis on a new assembly has been done but the gene build has not been completed. Owing to the preliminary nature of the data, Pre-Ensembl provides views of the assembly, BLAST against the assembly and download of portions of the assembly - and little else. A number of ready-made tools for processing your data are also available. In general a full Ensembl release takes months depending on how complex the data are and the time constraints of people in the team. Occasionally a more complete gene build will be released on this site, but without any comparative genomics, variation or other additional data. Many other species with fully annotated genomic data, more website features and documentation are available at www.ensembl.org

Proper citation: Pre Ensembl (RRID:SCR_006766) 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://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://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://Mar2008.archive.ensembl.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website).

Proper citation: Ensembl Genome Browser (RRID:SCR_013367) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/

Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request.

Proper citation: Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) 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.debian.org

Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application.

Proper citation: Debian (RRID:SCR_006638) 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

http://biit.cs.ut.ee/gprofiler/

Web server for functional enrichment analysis and conversions of gene lists. Web based tool for functional profiling of gene lists from large scale experiments. Has web interface with powerful visualization. Used for analyzing data from any organism.

Proper citation: g:Profiler (RRID:SCR_006809) Copy   

•   Source: SciCrunch Registry

http://www.vbase2.org/

Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse. It presents V gene sequences extracted from the EMBL nucleotide sequence database and Ensembl together with links to the respective source sequences. Based on the properties of the source sequences, V genes are classified into 3 different classes: * Class 1: genomic and rearranged evidence * Class 2: genomic evidence only * Class 3: rearranged evidence only This allows careful sequence quality validation by the user. References to other immunological databases ( KABAT, IMGT/LIGM and VBASE ) are given to provide all public annotation data for each V gene. The VBASE2 database can be accessed either by the Direct Query interface or by the DNAPLOT Query interface. The Sequences given by the user are aligned with DNAPLOT against the VBASE2 database. Direct Query allows to enter sequence IDs and names (Field 1), choose species, locus, V gene family and class (Field 2) or search for 100% sequences (Field 3). At the DNAPLOT Query, the sequences given by the user are aligned with DNAPLOT against the VBASE2 database. The DNAPLOT program offers V gene nucleotide sequence alignment referring to the IMGT V gene unique numbering. The Quick Search can be used either for Direct Query to search for sequence IDs and V gene names or for DNAPLOT Query for up to 5 sequences. The new Fab Analysis allows you to align Fab, scFab, scAb or scFv sequences with DNAPLOT against the VBASE2 database, where both heavy and light chain are analyzed.

Proper citation: VBASE2 (RRID:SCR_007082) Copy   

•   Source: SciCrunch Registry

http://www.blueprint-epigenome.eu/

Consortium to further the understanding of how genes are activated or repressed in both healthy and diseased human cells with a focus on distinct types of haematopoietic cells from healthy individuals and on their malignant leukemic counterparts. They will generate at least 100 reference epigenomes and study them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease. Reference epigenomes will be generated by state-of-the-art technologies from highly purified cells for a comprehensive set of epigenetic marks in accordance with quality standards set by International Human Epigenome Consortium (IHEC). Access to the data is provided as well as the protocols used to collect the different blood cell types, to perform the different types of epigenomic analyses, etc.). This resource-generating activity will be complemented by hypothesis-driven research into blood-based diseases, including common leukemias and autoimmune disease (Type 1 Diabetes), by discovery and validation of epigenetic markers for diagnostic use and by epigenetic target identification. Since epigenetic changes are reversible, they can be targets for the development of novel and more individualized medical treatments. The involvement of companies will energize epigenomic research in the private sector by the development of smart technologies for better diagnostic tests and by identifying new targets for compounds. Thus the results of the project may lead to targeted diagnostics, new treatments and preventive measures for specific diseases in individual patients, an approach known as "personalized medicine". The Blueprint Data Access Committee will consider applications for access to data sets stored in the European Genome-phenome Archive (EGA) when authorized to do so by the Blueprint consortium and the holders of the original consent documents. Access is conditional upon availability of samples and/or data and signed agreement by the researcher(s) and the responsible employing Institution to abide by policies related to publication, data disposal, ethical approval and confidentiality. At EBI, the ftp site with the data can be found. You can either opt to link to the track hubs yourself or you can add the track hub to a genome browser - UCSC or ENSEMBL. Also Meta Data files and README are available. The data can also be accessed via the BIOMART system.

Proper citation: Blueprint Epigenome (RRID:SCR_003844) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/resolver/SCR_002250

THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.

Proper citation: OMICtools (RRID:SCR_002250) Copy   

•   Source: SciCrunch Registry

https://bio.tools

Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information.

Proper citation: bio.tools (RRID:SCR_014695) Copy   

•   Source: SciCrunch Registry

https://www.hmtphenome.uniba.it

Collection of data about variants, genes, phenotypes and diseases involved in mitochondrial functionality. Users can search for variant position, gene, phenotype or disease and retrieve all related information through integrated network of biological entities.

Proper citation: HmtPhenome (RRID:SCR_017289) Copy   

•   Source: SciCrunch Registry