RESUMEN
Proteins seldom function individually. Instead, they interact with other proteins or nucleic acids to form stable macromolecular complexes that play key roles in important cellular processes and pathways. One of the goals of Saccharomyces Genome Database (SGD; www.yeastgenome.org) is to provide a complete picture of budding yeast biological processes. To this end, we have collaborated with the Molecular Interactions team that provides the Complex Portal database at EMBL-EBI to manually curate the complete yeast complexome. These data, from a total of 589 complexes, were previously available only in SGD's YeastMine data warehouse (yeastmine.yeastgenome.org) and the Complex Portal (www.ebi.ac.uk/complexportal). We have now incorporated these macromolecular complex data into the SGD core database and designed complex-specific reports to make these data easily available to researchers. These web pages contain referenced summaries focused on the composition and function of individual complexes. In addition, detailed information about how subunits interact within the complex, their stoichiometry and the physical structure are displayed when such information is available. Finally, we generate network diagrams displaying subunits and Gene Ontology annotations that are shared between complexes. Information on macromolecular complexes will continue to be updated in collaboration with the Complex Portal team and curated as more data become available.
Asunto(s)
ADN de Hongos , Bases de Datos Genéticas , Proteínas Fúngicas , Genoma Fúngico/genética , Saccharomyces/genética , ADN de Hongos/química , ADN de Hongos/genética , ADN de Hongos/metabolismo , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Proteínas Fúngicas/metabolismo , GenómicaRESUMEN
Database URL: http://www.yeastgenome.org.
Asunto(s)
Curaduría de Datos/métodos , Bases de Datos de Ácidos Nucleicos , Genoma Fúngico , Modelos Teóricos , Saccharomyces cerevisiae/genética , Curaduría de Datos/normasRESUMEN
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and to provide this wealth of information to advance, in many ways, research on other organisms, even those as evolutionarily distant as humans. To build such a bridge between biological kingdoms, SGD is curating data regarding yeast-human complementation, in which a human gene can successfully replace the function of a yeast gene, and/or vice versa. These data are manually curated from published literature, made available for download, and incorporated into a variety of analysis tools provided by SGD.
Asunto(s)
Bases de Datos Genéticas , Genoma Fúngico , Saccharomyces cerevisiae/genética , Predicción , Ontología de Genes , Genes Fúngicos , Genoma Humano , Humanos , Mutación , Especificidad de la EspecieRESUMEN
The Candida Genome Database (CGD, http://www.candidagenome.org/) is a freely available online resource that provides gene, protein and sequence information for multiple Candida species, along with web-based tools for accessing, analyzing and exploring these data. The mission of CGD is to facilitate and accelerate research into Candida pathogenesis and biology, by curating the scientific literature in real time, and connecting literature-derived annotations to the latest version of the genomic sequence and its annotations. Here, we report the incorporation into CGD of Assembly 22, the first chromosome-level, phased diploid assembly of the C. albicans genome, coupled with improvements that we have made to the assembly using additional available sequence data. We also report the creation of systematic identifiers for C. albicans genes and sequence features using a system similar to that adopted by the yeast community over two decades ago. Finally, we describe the incorporation of JBrowse into CGD, which allows online browsing of mapped high throughput sequencing data, and its implementation for several RNA-Seq data sets, as well as the whole genome sequencing data that was used in the construction of Assembly 22.
Asunto(s)
Candida/genética , Biología Computacional/métodos , Bases de Datos de Ácidos Nucleicos , Genoma Fúngico , Programas Informáticos , Proteínas Fúngicas/química , Proteínas Fúngicas/genética , Genómica/métodos , Secuenciación de Nucleótidos de Alto Rendimiento , Anotación de Secuencia Molecular , Sistemas de Lectura Abierta , Navegador WebRESUMEN
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. To provide a wider scope of genetic and phenotypic variation in yeast, the genome sequences and their corresponding annotations from 11 alternative S. cerevisiae reference strains have been integrated into SGD. Genomic and protein sequence information for genes from these strains are now available on the Sequence and Protein tab of the corresponding Locus Summary pages. We illustrate how these genome sequences can be utilized to aid our understanding of strain-specific functional and phenotypic differences.Database URL: www.yeastgenome.org.
Asunto(s)
Bases de Datos Genéticas , Genoma Fúngico/genética , Genómica/métodos , Saccharomyces/genética , Anotación de Secuencia Molecular , Reproducibilidad de los Resultados , Saccharomyces cerevisiae/genética , Interfaz Usuario-ComputadorRESUMEN
In recent years, thousands of Saccharomyces cerevisiae genomes have been sequenced to varying degrees of completion. The Saccharomyces Genome Database (SGD) has long been the keeper of the original eukaryotic reference genome sequence, which was derived primarily from S. cerevisiae strain S288C. Because new technologies are pushing S. cerevisiae annotation past the limits of any system based exclusively on a single reference sequence, SGD is actively working to expand the original S. cerevisiae systematic reference sequence from a single genome to a multi-genome reference panel. We first commissioned the sequencing of additional genomes and their automated analysis using the AGAPE pipeline. Here we describe our curation strategy to produce manually reviewed high-quality genome annotations in order to elevate 11 of these additional genomes to Reference status. Database URL: http://www.yeastgenome.org/.
Asunto(s)
Genoma Fúngico , Saccharomyces cerevisiae/genética , Automatización , Secuencia de Bases , Minería de Datos , Bases de Datos Genéticas , Sistemas de Lectura Abierta/genética , Estándares de ReferenciaRESUMEN
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer.
Asunto(s)
Bases de Datos Genéticas , Variación Genética , Genoma Fúngico , Saccharomyces cerevisiae/genética , Anotación de Secuencia Molecular , Alineación de Secuencia , Análisis de Secuencia de ADN , Análisis de Secuencia de Proteína , Interfaz Usuario-ComputadorRESUMEN
InterMine is a data integration warehouse and analysis software system developed for large and complex biological data sets. Designed for integrative analysis, it can be accessed through a user-friendly web interface. For bioinformaticians, extensive web services as well as programming interfaces for most common scripting languages support access to all features. The web interface includes a useful identifier look-up system, and both simple and sophisticated search options. Interactive results tables enable exploration, and data can be filtered, summarized, and browsed. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other entities. InterMine databases have been developed for the major model organisms, budding yeast, nematode worm, fruit fly, zebrafish, mouse, and rat together with a newly developed human database. Here, we describe how this has facilitated interoperation and development of cross-organism analysis tools and reports. InterMine as a data exploration and analysis tool is also described. All the InterMine-based systems described in this article are resources freely available to the scientific community.
Asunto(s)
Bases de Datos Factuales , Programas Informáticos , Animales , Biología Computacional/métodos , Bases de Datos Genéticas , Genómica , Humanos , Internet , Integración de Sistemas , Interfaz Usuario-ComputadorRESUMEN
The Candida Genome Database (CGD, http://www.candidagenome.org/) is a freely available online resource that provides gene, protein and sequence information for multiple Candida species, along with web-based tools for accessing, analyzing and exploring these data. The goal of CGD is to facilitate and accelerate research into Candida pathogenesis and biology. The CGD Web site is organized around Locus pages, which display information collected about individual genes. Locus pages have multiple tabs for accessing different types of information; the default Summary tab provides an overview of the gene name, aliases, phenotype and Gene Ontology curation, whereas other tabs display more in-depth information, including protein product details for coding genes, notes on changes to the sequence or structure of the gene and a comprehensive reference list. Here, in this update to previous NAR Database articles featuring CGD, we describe a new tab that we have added to the Locus page, entitled the Homology Information tab, which displays phylogeny and gene similarity information for each locus.
Asunto(s)
Candida/genética , Bases de Datos Genéticas , Proteínas Fúngicas/química , Genoma Fúngico , Filogenia , Candida/clasificación , Proteínas Fúngicas/genética , Internet , Homología de Secuencia de AminoácidoRESUMEN
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the community resource for genomic, gene and protein information about the budding yeast Saccharomyces cerevisiae, containing a variety of functional information about each yeast gene and gene product. We have recently added regulatory information to SGD and present it on a new tabbed section of the Locus Summary entitled 'Regulation'. We are compiling transcriptional regulator-target gene relationships, which are curated from the literature at SGD or imported, with permission, from the YEASTRACT database. For nearly every S. cerevisiae gene, the Regulation page displays a table of annotations showing the regulators of that gene, and a graphical visualization of its regulatory network. For genes whose products act as transcription factors, the Regulation page also shows a table of their target genes, accompanied by a Gene Ontology enrichment analysis of the biological processes in which those genes participate. We additionally synthesize information from the literature for each transcription factor in a free-text Regulation Summary, and provide other information relevant to its regulatory function, such as DNA binding site motifs and protein domains. All of the regulation data are available for querying, analysis and download via YeastMine, the InterMine-based data warehouse system in use at SGD.
Asunto(s)
Bases de Datos Genéticas , Regulación Fúngica de la Expresión Génica , Genoma Fúngico , Saccharomyces cerevisiae/genética , Sitios de Unión , Redes Reguladoras de Genes , Internet , Estructura Terciaria de Proteína , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Factores de Transcripción/química , Factores de Transcripción/metabolismo , Transcripción GenéticaRESUMEN
The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called "S288C 2010," was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science.
Asunto(s)
Genoma Fúngico , Saccharomyces cerevisiae/genética , Mapeo Cromosómico , Bases de Datos Factuales , Internet , Sistemas de Lectura Abierta , Análisis de Secuencia de ADN , Interfaz Usuario-ComputadorRESUMEN
The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available web-based resource that was designed for Aspergillus researchers and is also a valuable source of information for the entire fungal research community. In addition to being a repository and central point of access to genome, transcriptome and polymorphism data, AspGD hosts a comprehensive comparative genomics toolbox that facilitates the exploration of precomputed orthologs among the 20 currently available Aspergillus genomes. AspGD curators perform gene product annotation based on review of the literature for four key Aspergillus species: Aspergillus nidulans, Aspergillus oryzae, Aspergillus fumigatus and Aspergillus niger. We have iteratively improved the structural annotation of Aspergillus genomes through the analysis of publicly available transcription data, mostly expressed sequenced tags, as described in a previous NAR Database article (Arnaud et al. 2012). In this update, we report substantive structural annotation improvements for A. nidulans, A. oryzae and A. fumigatus genomes based on recently available RNA-Seq data. Over 26 000 loci were updated across these species; although those primarily comprise the addition and extension of untranslated regions (UTRs), the new analysis also enabled over 1000 modifications affecting the coding sequence of genes in each target genome.
Asunto(s)
Aspergillus/genética , Bases de Datos Genéticas , Genoma Fúngico , Anotación de Secuencia Molecular , Perfilación de la Expresión Génica , Genes Fúngicos , Internet , Análisis de Secuencia de ARNRESUMEN
Model organisms are widely used for understanding basic biology, and have significantly contributed to the study of human disease. In recent years, genomic analysis has provided extensive evidence of widespread conservation of gene sequence and function amongst eukaryotes, allowing insights from model organisms to help decipher gene function in a wider range of species. The InterMOD consortium is developing an infrastructure based around the InterMine data warehouse system to integrate genomic and functional data from a number of key model organisms, leading the way to improved cross-species research. So far including budding yeast, nematode worm, fruit fly, zebrafish, rat and mouse, the project has set up data warehouses, synchronized data models, and created analysis tools and links between data from different species. The project unites a number of major model organism databases, improving both the consistency and accessibility of comparative research, to the benefit of the wider scientific community.
Asunto(s)
Genoma , Modelos Genéticos , Animales , Bases de Datos Factuales , Bases de Datos Genéticas , Genómica/métodosRESUMEN
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) provides high-quality curated genomic, genetic, and molecular information on the genes and their products of the budding yeast Saccharomyces cerevisiae. To accommodate the increasingly complex, diverse needs of researchers for searching and comparing data, SGD has implemented InterMine (http://www.InterMine.org), an open source data warehouse system with a sophisticated querying interface, to create YeastMine (http://yeastmine.yeastgenome.org). YeastMine is a multifaceted search and retrieval environment that provides access to diverse data types. Searches can be initiated with a list of genes, a list of Gene Ontology terms, or lists of many other data types. The results from queries can be combined for further analysis and saved or downloaded in customizable file formats. Queries themselves can be customized by modifying predefined templates or by creating a new template to access a combination of specific data types. YeastMine offers multiple scenarios in which it can be used such as a powerful search interface, a discovery tool, a curation aid and also a complex database presentation format. DATABASE URL: http://yeastmine.yeastgenome.org.
Asunto(s)
Sistemas de Administración de Bases de Datos , Bases de Datos Genéticas , Genoma Fúngico , Saccharomyces cerevisiae/genética , Internet , Interfaz Usuario-ComputadorRESUMEN
The Candida Genome Database (CGD, http://www.candidagenome.org/) is an internet-based resource that provides centralized access to genomic sequence data and manually curated functional information about genes and proteins of the fungal pathogen Candida albicans and other Candida species. As the scope of Candida research, and the number of sequenced strains and related species, has grown in recent years, the need for expanded genomic resources has also grown. To answer this need, CGD has expanded beyond storing data solely for C. albicans, now integrating data from multiple species. Herein we describe the incorporation of this multispecies information, which includes curated gene information and the reference sequence for C. glabrata, as well as orthology relationships that interconnect Locus Summary pages, allowing easy navigation between genes of C. albicans and C. glabrata. These orthology relationships are also used to predict GO annotations of their products. We have also added protein information pages that display domains, structural information and physicochemical properties; bibliographic pages highlighting important topic areas in Candida biology; and a laboratory strain lineage page that describes the lineage of commonly used laboratory strains. All of these data are freely available at http://www.candidagenome.org/. We welcome feedback from the research community at candida-curator@lists.stanford.edu.
Asunto(s)
Candida/genética , Bases de Datos Genéticas , Proteínas Fúngicas/química , Genes Fúngicos , Genoma Fúngico , Candida albicans/genética , Candida glabrata/genética , Genómica , Programas InformáticosRESUMEN
The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available, web-based resource for researchers studying fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD curators have now completed comprehensive review of the entire published literature about Aspergillus nidulans and Aspergillus fumigatus, and this annotation is provided with streamlined, ortholog-based navigation of the multispecies information. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. AspGD also provides resources to foster interaction and dissemination of community information and resources. We welcome and encourage feedback at aspergillus-curator@lists.stanford.edu.
Asunto(s)
Aspergillus/genética , Bases de Datos Genéticas , Genoma Fúngico , Aspergillus fumigatus/genética , Aspergillus nidulans/genética , Genes Fúngicos , Genómica , Anotación de Secuencia MolecularRESUMEN
The Saccharomyces Genome Database (SGD, http://www.yeastgenome.org) is the community resource for the budding yeast Saccharomyces cerevisiae. The SGD project provides the highest-quality manually curated information from peer-reviewed literature. The experimental results reported in the literature are extracted and integrated within a well-developed database. These data are combined with quality high-throughput results and provided through Locus Summary pages, a powerful query engine and rich genome browser. The acquisition, integration and retrieval of these data allow SGD to facilitate experimental design and analysis by providing an encyclopedia of the yeast genome, its chromosomal features, their functions and interactions. Public access to these data is provided to researchers and educators via web pages designed for optimal ease of use.
Asunto(s)
Bases de Datos Genéticas , Genoma Fúngico , Saccharomyces cerevisiae/genética , Genes Fúngicos , Genómica , Secuenciación de Nucleótidos de Alto Rendimiento , Anotación de Secuencia Molecular , Fenotipo , Programas Informáticos , Terminología como AsuntoRESUMEN
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. The information in SGD includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary literature from which these data are derived. Here we describe how published phenotypes and genetic interaction data are annotated and displayed in SGD.
Asunto(s)
Biología Computacional/métodos , Bases de Datos de Ácidos Nucleicos , Genoma Fúngico , Mutación , Saccharomyces cerevisiae/genética , Biología Computacional/tendencias , ADN de Hongos , Bases de Datos Genéticas , Bases de Datos de Proteínas , Genes Fúngicos , Almacenamiento y Recuperación de la Información/métodos , Internet , Fenotipo , Estructura Terciaria de Proteína , Programas InformáticosRESUMEN
The Candida Genome Database (CGD, http://www.candidagenome.org/) provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. Herein, we describe two recently added features, Candida Biochemical Pathways and the Textpresso full-text literature search tool. The Biochemical Pathways tool provides visualization of metabolic pathways and analysis tools that facilitate interpretation of experimental data, including results of large-scale experiments, in the context of Candida metabolism. Textpresso for Candida allows searching through the full-text of Candida-specific literature, including clinical and epidemiological studies.
Asunto(s)
Candida albicans/genética , Biología Computacional/métodos , Bases de Datos Genéticas , Bases de Datos de Ácidos Nucleicos , Genoma Fúngico , Biología Computacional/tendencias , ADN de Hongos/genética , Bases de Datos de Proteínas , Genes Fúngicos , Almacenamiento y Recuperación de la Información/métodos , Internet , Sistemas de Lectura Abierta , Estructura Terciaria de Proteína , Programas Informáticos , Interfaz Usuario-ComputadorRESUMEN
The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli. AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively refine and improve structural gene annotations across multiple Aspergillus species, and web-based research tools for accessing and exploring the data. All of these data are freely available at http://www.aspgd.org. We welcome feedback from users and the research community at aspergillus-curator@genome.stanford.edu.