RESUMEN
The Génolevures online database (http://cbi.labri.fr/Genolevures/) provides tools and data relative to 4 complete and 10 partial genome sequences determined and manually annotated by the Génolevures Consortium, to facilitate comparative genomic studies of hemiascomycetous yeasts. With their relatively small and compact genomes, yeasts offer a unique opportunity for exploring eukaryotic genome evolution. The new version of the Génolevures database provides truly complete (subtelomere to subtelomere) chromosome sequences, 25 000 protein-coding and tRNA genes, and in silico analyses for each gene element. A new feature of the database is a novel collection of conserved multi-species protein families and their mapping to metabolic pathways, coupled with an advanced search feature. Data are presented with a focus on relations between genes and genomes: conservation of genes and gene families, speciation, chromosomal reorganization and synteny. The Génolevures site includes an area for specific studies by members of its international community.
Asunto(s)
Bases de Datos Genéticas , Genoma Fúngico , Levaduras/genética , Evolución Molecular , Proteínas Fúngicas/química , Proteínas Fúngicas/clasificación , Proteínas Fúngicas/genética , Genómica , Internet , Programas Informáticos , Integración de Sistemas , Interfaz Usuario-ComputadorRESUMEN
Mathematical models of biological processes for the model yeast Saccharomyces cerevisiae are the subject of intensive effort and are available in increasing numbers. An open question is whether such models are informative for related yeasts of biotechnological and medical interest that will not themselves benefit from an equivalent effort. In this study, we assess a method for extrapolating reference models to other completely sequenced yeasts, using a combination of graph-theoretic analysis and reliable identification of homologous genes using Génolevures protein families. In this first assessment, we focus on subtractive modeling, identified through the correlated loss of input and output ports in metabolic pathways. We confirm that the major, highly connected, pathways of central metabolism are conserved and might be universal. In 60-80% of our results, further analysis is not required to determine whether the pathway is lost or conserved, so that our method can be systematically applied as a first step in developing species-specific models.
Asunto(s)
Biología Computacional/métodos , Genes Fúngicos , Redes y Vías Metabólicas , Modelos Biológicos , Levaduras/fisiología , Biología Computacional/instrumentación , Regulación Fúngica de la Expresión Génica/fisiología , Genoma FúngicoRESUMEN
UNLABELLED: ProViz is a tool for the visualization of protein-protein interaction networks, developed by the IntAct European project. It provides facilities for navigating in large graphs and exploring biologically relevant features, and adopts emerging standards such as GO and PSI-MI. AVAILABILITY: ProViz is available under the GPL and may be freely downloaded. Source code and binaries are available at http://cbi.labri.fr/eng/proviz.htm CONTACT: david.sherman@labri.fr
Asunto(s)
Documentación/métodos , Regulación de la Expresión Génica/fisiología , Modelos Biológicos , Mapeo de Interacción de Proteínas/métodos , Transducción de Señal/fisiología , Programas Informáticos , Factores de Transcripción/metabolismo , Interfaz Usuario-Computador , Gráficos por Computador , Bases de Datos de Proteínas , Almacenamiento y Recuperación de la Información/métodosRESUMEN
UNLABELLED: AliasServer provides services that facilitate the assembly of data or datasets that make use of different identifiers for refering to the same protein. This resource relies on a database which contains, for a given organism, a non-redundant list of protein sequences associated with a set of aliases. AVAILABILITY: AliasServer is available as an interactive Web server at http://cbi.labri.fr/outils/alias/ and as a web service using a SOAP interface. The complete tool, including sources and data, is available for local installations upon request. SUPPLEMENTARY INFORMATION: Technical documentation is available at http://cbi.labri.fr/outils/alias/asdoc.pdf
Asunto(s)
Sistemas de Administración de Bases de Datos , Bases de Datos de Proteínas , Almacenamiento y Recuperación de la Información/métodos , Internet , Proteínas/química , Proteínas/clasificación , Interfaz Usuario-Computador , Algoritmos , Documentación/métodos , Procesamiento de Lenguaje Natural , Alineación de Secuencia/métodos , Análisis de Secuencia de Proteína/métodos , Programas Informáticos , Vocabulario ControladoRESUMEN
SUMMARY: IPPRED is a web based server to infer protein-protein interactions through homology search between candidate proteins and those described as interacting. This simple inference allows to propose or to validate potential interactions. AVAILABILITY: IPPRED is freely available at http://cbi.labri.fr/outils/ippred/.