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Ensembl Genomes is a scientific project to provide genome-scale data from non-vertebrate species. The project is run by the European Bioinformatics Institute, and was launched in 2009 using the Ensembl technology. The main objective of the Ensembl Genomes database is to complement the main Ensembl database by introducing five additional web pages to include genome data for bacteria, fungi, invertebrate metazoa, plants, and protists. For each of the domains, the Ensembl tools are available for manipulation, analysis and visualization of genome data. Most Ensembl Genomes data is stored in MySQL relational databases and can be accessed by the Ensembl Perl API, virtual machines or online. Ensembl Genomes is an open project, and most of the code, tools, and data are available to the public. Ensembl and Ensembl Genomes software uses a "permissive Apache-style open-source" license, making it free for all users. == Displaying genomic data == The key feature of Ensembl Genomes is its graphical interface, which allows users to scroll through a genome and observe the relative location of features such as conceptual annotation (e.g. genes, SNP loci), sequence patterns (e.g. repeats) and experimental data (e.g. sequences and external sequence features mapped onto the genome). Graphical views are available for varying levels of resolution from an entire karyotype, down to the sequence of a single exon. Information for a genome is spread over four tabs, a species page, a ‘Location’ tab, a ‘Gene’ tab and a ‘Transcript’ tab, each providing information at a higher resolution. Searching for a particular species using Ensembl Genomes redirects to the species page. Often, a brief description of the species is provided, as well as links to further information and statistics about the genome, the graphical interface and some of the tools available. A karyotype is available for some species in Ensembl Genomes.〔(【引用サイトリンク】Whole Genome )〕 If the karyotype is available there will be a link to it in the Gene Assembly section of the species page. Alternatively if users are in the ‘Location’ tab they can also view the karyotype by selecting ‘Whole genome’ in the left-hand menu. Users can click on a location within the karyotype to zoom in to one specific chromosome or a genomic region.〔 This will open the ‘Location’ Tab. In the 'Location' tab, users can browse genes, variations, sequence conservation, and other types of annotation along the genome.〔(【引用サイトリンク】Frequently Asked Questions )〕 The 'Region in detail' is highly configurable and scalable, and users can choose what they want to see by clicking on the 'Configure this page' button at the bottom of the left-hand menu. By adding and removing tracks users will be able to select the type of data they want to have included in the displays.〔 Data from the following categories can be easily added or removed from this 'Location' tab view: 'Sequence and assembly', 'Genes and transcripts', 'mRNA and protein alignments', 'Other DNA alignments', 'Germline variation', 'Comparative genomics', among others.〔 Users can also change the display options such as the width.〔 A further option allows users to reset the configuration back to the default settings.〔 More specific information about a select gene can be found in the ‘Gene’ tab. Users can get to this page by searching for desired gene in the search bar and clicking on the gene ID or by clicking on one of the genes shown in the ‘Location’ tab view. The ‘Gene’ tab contains gene-specific information such as gene structure, number of transcripts, position on the chromosome and homology information in the form of gene trees. This information can be accessed via the menu on the left-hand side. A 'Transcript' tab will also appear when a user chooses to view a gene. The 'Transcript' tab contains much of the same information as the 'Gene' tab, however it is focused on only one transcript. 抄文引用元・出典: フリー百科事典『 ウィキペディア（Wikipedia）』 ■ウィキペディアで「Ensembl Genomes is a scientific project to provide genome-scale data from non-vertebrate species.The project is run by the European Bioinformatics Institute, and was launched in 2009 using the Ensembl technology. The main objective of the Ensembl Genomes database is to complement the main Ensembldatabase by introducing five additional web pages to include genome data for bacteria, fungi, invertebrate metazoa, plants, and protists. For each of the domains, the Ensembl tools are available for manipulation, analysis and visualization of genome data. Most Ensembl Genomes data is stored in MySQL relational databases and can be accessed by the Ensembl Perl API, virtual machines or online.Ensembl Genomes is an open project, and most of the code, tools, and data are available to the public. Ensembl and Ensembl Genomes software uses a "permissive Apache-style open-source" license, making it free for all users.== Displaying genomic data ==The key feature of Ensembl Genomes is its graphical interface, which allows users to scroll through a genome and observe the relative location of features such as conceptual annotation (e.g. genes, SNP loci), sequence patterns (e.g. repeats) and experimental data (e.g. sequences and external sequence features mapped onto the genome). Graphical views are available for varying levels of resolution from an entire karyotype, down to the sequence of a single exon. Information for a genome is spread over four tabs, a species page, a ‘Location’ tab, a ‘Gene’ tab and a ‘Transcript’ tab, each providing information at a higher resolution.Searching for a particular species using Ensembl Genomes redirects to the species page. Often, a brief description of the species is provided, as well as links to further information and statistics about the genome, the graphical interface and some of the tools available.A karyotype is available for some species in Ensembl Genomes.(【引用サイトリンク】Whole Genome ) If the karyotype is available there will be a link to it in the Gene Assembly section of the species page. Alternatively if users are in the ‘Location’ tab they can also view the karyotype by selecting ‘Whole genome’ in the left-hand menu. Users can click on a location within the karyotype to zoom in to one specific chromosome or a genomic region. This will open the ‘Location’ Tab.In the 'Location' tab, users can browse genes, variations, sequence conservation, and other types of annotation along the genome.(【引用サイトリンク】Frequently Asked Questions ) The 'Region in detail' is highly configurable and scalable, and users can choose what they want to see by clicking on the 'Configure this page' button at the bottom of the left-hand menu. By adding and removing tracks users will be able to select the type of data they want to have included in the displays. Data from the following categories can be easily added or removed from this 'Location' tab view: 'Sequence and assembly', 'Genes and transcripts', 'mRNA and protein alignments', 'Other DNA alignments', 'Germline variation', 'Comparative genomics', among others. Users can also change the display options such as the width. A further option allows users to reset the configuration back to the default settings.More specific information about a select gene can be found in the ‘Gene’ tab. Users can get to this page by searching for desired gene in the search bar and clicking on the gene ID or by clicking on one of the genes shown in the ‘Location’ tab view. The ‘Gene’ tab contains gene-specific information such as gene structure, number of transcripts, position on the chromosome and homology information in the form of gene trees. This information can be accessed via the menu on the left-hand side.A 'Transcript' tab will also appear when a user chooses to view a gene. The 'Transcript' tab contains much of the same information as the 'Gene' tab, however it is focused on only one transcript.」の詳細全文を読む スポンサード リンク
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