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1.
Nucleic Acids Res ; 48(D1): D689-D695, 2020 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-31598706

RESUMO

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.


Assuntos
Biologia Computacional/métodos , Bases de Dados Genéticas , Variação Genética , Genoma Bacteriano , Genoma Fúngico , Genoma de Planta , Algoritmos , Animais , Caenorhabditis elegans/genética , Genômica , Internet , Anotação de Sequência Molecular , Fenótipo , Plantas/genética , Valores de Referência , Software , Interface Usuário-Computador
2.
Nucleic Acids Res ; 45(D1): D635-D642, 2017 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-27899575

RESUMO

Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license.


Assuntos
Biologia Computacional/métodos , Bases de Dados Genéticas , Genômica/métodos , Ferramenta de Busca , Software , Navegador , Animais , Mineração de Dados , Evolução Molecular , Regulação da Expressão Gênica , Variação Genética , Genoma Humano , Humanos , Anotação de Sequência Molecular , Especificidade da Espécie , Vertebrados
3.
Nucleic Acids Res ; 44(D1): D688-93, 2016 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-26476449

RESUMO

PhytoPath (www.phytopathdb.org) is a resource for genomic and phenotypic data from plant pathogen species, that integrates phenotypic data for genes from PHI-base, an expertly curated catalog of genes with experimentally verified pathogenicity, with the Ensembl tools for data visualization and analysis. The resource is focused on fungi, protists (oomycetes) and bacterial plant pathogens that have genomes that have been sequenced and annotated. Genes with associated PHI-base data can be easily identified across all plant pathogen species using a BioMart-based query tool and visualized in their genomic context on the Ensembl genome browser. The PhytoPath resource contains data for 135 genomic sequences from 87 plant pathogen species, and 1364 genes curated for their role in pathogenicity and as targets for chemical intervention. Support for community annotation of gene models is provided using the WebApollo online gene editor, and we are working with interested communities to improve reference annotation for selected species.


Assuntos
Bases de Dados Genéticas , Genômica , Interações Hospedeiro-Patógeno/genética , Doenças das Plantas/microbiologia , Genes Bacterianos , Genes Fúngicos , Genoma Bacteriano , Genoma Fúngico , Oomicetos/genética , Fenótipo , Alinhamento de Sequência
4.
Nucleic Acids Res ; 44(D1): D574-80, 2016 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-26578574

RESUMO

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces.


Assuntos
Bases de Dados Genéticas , Genoma Bacteriano , Genoma Fúngico , Genoma de Planta , Invertebrados/genética , Animais , Diploide , Eucariotos/genética , Variação Genética , Genoma , Poliploidia , Alinhamento de Sequência
5.
Nucleic Acids Res ; 43(Database issue): D656-61, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25361970

RESUMO

PomBase (http://www.pombase.org) is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven research. It provides users easy access to data ranging from the sequence level, to molecular and phenotypic annotations, through to the display of genome-wide high-throughput studies. Recent improvements to the site extend annotation specificity, improve usability and allow for monthly data updates. Both in-house curators and community researchers provide manually curated data to PomBase. The genome browser provides access to published high-throughput data sets and the genomes of three additional Schizosaccharomyces species (Schizosaccharomyces cryophilus, Schizosaccharomyces japonicus and Schizosaccharomyces octosporus).


Assuntos
Bases de Dados Genéticas , Schizosaccharomyces/genética , Expressão Gênica , Ontologia Genética , Genes Fúngicos , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Internet , Anotação de Sequência Molecular
6.
Nucleic Acids Res ; 43(W1): W50-6, 2015 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-25904632

RESUMO

RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/.


Assuntos
Elementos Reguladores de Transcrição , Software , Sítios de Ligação , Variação Genética , Genômica , Humanos , Internet , Motivos de Nucleotídeos , Fatores de Transcrição/metabolismo
7.
Nucleic Acids Res ; 40(Database issue): D695-9, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22039153

RESUMO

PomBase (www.pombase.org) is a new model organism database established to provide access to comprehensive, accurate, and up-to-date molecular data and biological information for the fission yeast Schizosaccharomyces pombe to effectively support both exploratory and hypothesis-driven research. PomBase encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets, and supports sophisticated user-defined queries. The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access. PomBase will provide user-friendly tools to promote curation by experts within the fission yeast community. This will make a key contribution to shaping its content and ensuring its comprehensiveness and long-term relevance.


Assuntos
Bases de Dados Genéticas , Schizosaccharomyces/genética , Genoma Fúngico , Genômica , Internet , Anotação de Sequência Molecular , Fenótipo
8.
Nucleic Acids Res ; 40(Database issue): D91-7, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22067447

RESUMO

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.


Assuntos
Bases de Dados Genéticas , Genômica , Animais , Genoma , Genoma Bacteriano , Genoma Fúngico , Genoma de Planta , Invertebrados/genética , Anotação de Sequência Molecular , Integração de Sistemas
9.
Methods Mol Biol ; 1533: 1-31, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-27987162

RESUMO

Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for 39 sequenced plant species. Available data includes genome sequence, gene models, functional annotation, and polymorphic loci; for the latter, additional information including population structure, individual genotypes, linkage, and phenotype data is available for some species. Comparative data is also available, including genomic alignments and "gene trees," which show the inferred evolutionary history of each gene family represented in the resource. Access to the data is provided through a genome browser, which incorporates many specialist interfaces for different data types, through a variety of programmatic interfaces, and via a specialist data mining tool supporting rapid filtering and retrieval of bulk data. Genomic data from many non-plant species, including those of plant pathogens, pests, and pollinators, is also available via the same interfaces through other divisions of Ensembl.Ensembl Plants is updated 4-6 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.eu ).


Assuntos
Biologia Computacional/métodos , Genoma de Planta , Genômica , Plantas/genética , Software , Mapeamento Cromossômico , Produtos Agrícolas/genética , Mineração de Dados/métodos , Bases de Dados Genéticas , Variação Genética , Genômica/métodos , Anotação de Sequência Molecular , Fenótipo , Interface Usuário-Computador , Navegador
10.
Methods Mol Biol ; 1374: 115-40, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26519403

RESUMO

Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species (currently 33). Data provided includes genome sequence, gene models, functional annotation, and polymorphic loci. Various additional information are provided for variation data, including population structure, individual genotypes, linkage, and phenotype data. In each release, comparative analyses are performed on whole genome and protein sequences, and genome alignments and gene trees are made available that show the implied evolutionary history of each gene family. Access to the data is provided through a genome browser incorporating many specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These access routes are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests, and pollinators.Ensembl Plants is updated 4-5 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.org ).


Assuntos
Biologia Computacional/métodos , Genômica/métodos , Plantas/genética , Mineração de Dados/métodos , Bases de Dados Genéticas , Genoma de Planta , Navegador
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