RESUMEN
New methods and tools are needed to exploit the unprecedented source of information made available by the completed and ongoing whole genome sequencing projects. The Narcisse database is dedicated to the study of genome conservation, from sequence similarities to conserved chromosomal segments or conserved syntenies, for a large number of animals, plants and bacterial completely sequenced genomes. The query interface, a comparative genome browser, enables to navigate between genome dotplots, comparative maps and sequence alignments. The Narcisse database can be accessed at http://narcisse.toulouse.inra.fr.
Asunto(s)
Bases de Datos de Ácidos Nucleicos , Sintenía , Animales , Secuencia de Bases , Mapeo Cromosómico , Secuencia Conservada , Genoma Bacteriano , Genoma de Planta , Genómica , Humanos , Internet , Ratas , Alineación de Secuencia , Interfaz Usuario-ComputadorRESUMEN
UNLABELLED: Large- and medium-scale computational molecular biology projects require accurate bioinformatics software and numerous heterogeneous biological databanks, which are distributed around the world. BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. We have developed workflows that handle some of the most commonly used bioinformatics databases. A set of scripts is also available for post-synchronization data treatment consisting of indexation or format conversion (for NCBI blast, SRS, EMBOSS, GCG, etc.). BioMAJ can be easily extended by personal homemade processing scripts. Source history can be kept via html reports containing statements of locally managed databanks. AVAILABILITY: http://biomaj.genouest.org. BioMAJ is free open software. It is freely available under the CECILL version 2 license.
Asunto(s)
Algoritmos , Sistemas de Administración de Bases de Datos , Bases de Datos Genéticas , Almacenamiento y Recuperación de la Información/métodos , Lenguajes de Programación , Programas Informáticos , Interfaz Usuario-Computador , Biología Computacional/métodosRESUMEN
ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences. Recent improvements include the use of three-dimensional (3D) information from the SCOP database; a completely redesigned web interface (http://www.toulouse.inra.fr/prodom.html); visualization of ProDom domains on 3D structures; coupling of ProDom analysis with the Geno3D homology modelling server; Bayesian inference of evolutionary scenarios for ProDom families. In addition, we have developed ProDom-SG, a ProDom-based server dedicated to the selection of candidate proteins for structural genomics.