BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations

BAliBASE is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The database contains high quality, manually constructed multiple sequence alignments together with detailed annotations. The alignments are all based on three-dimensional structural superpositions, with the exception of the transmembrane sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Here we describe version 2.0 of the database, which incorporates three new reference sets of alignments containing structural repeats, trans­membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. BAliBASE can be viewed at the web site http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html or can be downloaded from ftp://ftp-igbmc.u-strasbg.fr/pub/BAliBASE2/.

The Stanford Microarray Database

The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two immediate goals for SMD are to serve as a storage site for microarray data from ongoing research at Stanford University, and to facilitate the public dissemination of that data once published, or released by the researcher. Of paramount importance is the connection of microarray data with the biological data that pertains to the DNA deposited on the microarray (genes, clones etc.). SMD makes use of many public resources to connect expression information to the relevant biology, including SGD [Ball,C.A., Dolinski,K., Dwight,S.S., Harris,M.A., Issel-Tarver,L., Kasarskis,A., Scafe,C.R., Sherlock,G., Binkley,G., Jin,H. et al. (2000) Nucleic Acids Res., 28, 77–80], YPD and WormPD [Costanzo,M.C., Hogan,J.D., Cusick,M.E., Davis,B.P., Fancher,A.M., Hodges,P.E., Kondu,P., Lengieza,C., Lew-Smith,J.E., Lingner,C. et al. (2000) Nucleic Acids Res., 28, 73–76], Unigene [Wheeler,D.L., Chappey,C., Lash,A.E., Leipe,D.D., Madden,T.L., Schuler,G.D., Tatusova,T.A. and Rapp,B.A. (2000) Nucleic Acids Res., 28, 10–14], dbEST [Boguski,M.S., Lowe,T.M. and Tolstoshev,C.M. (1993) Nature Genet., 4, 332–333] and SWISS-PROT [Bairoch,A. and Apweiler,R. (2000) Nucleic Acids Res., 28, 45–48] and can be accessed at http://genome-www.stanford.edu/microarray.

HC Forum®: a web site based on an international human cytogenetic database

Familial structural rearrangements of chromosomes represent a factor of malformation risk that could vary over a large range, making genetic counseling difficult. However, they also represent a powerful tool for increasing knowledge of the genome, particularly by studying breakpoints and viable imbalances of the genome. We have developed a collaborative database that now includes data on more than 4100 families, from which we have developed a web site called HC Forum® (http://HCForum.imag.fr). It offers geneticists assistance in diagnosis and in genetic counseling by assessing the malformation risk with statistical models. For researchers, interactive interfaces exhibit the distribution of chromosomal breakpoints and of the genome regions observed at birth in trisomy or in monosomy. Dedicated tools including an interactive pedigree allow electronic submission of data, which will be anonymously shown in a forum for discussions. After validation, data are definitively registered in the database with the email of the sender, allowing direct location of biological material. Thus HC Forum® constitutes a link between diagnosis laboratories and genome research centers, and after 1 year, more than 700 users from about 40 different countries already exist.

The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant

Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).

The RESID Database of protein structure modifications and the NRL-3D Sequence–Structure Database

The RESID Database is a comprehensive collection of annotations and structures for protein post-translational modifications including N-terminal, C-terminal and peptide chain cross-link modifications. The RESID Database includes systematic and frequently observed alternate names, Chemical Abstracts Service registry numbers, atomic formulas and weights, enzyme activities, taxonomic range, keywords, literature citations with database cross-references, structural diagrams and molecular models. The NRL-3D Sequence–Structure Database is derived from the three-dimensional structure of proteins deposited with the Research Collaboratory for Structural Bioinformatics Protein Data Bank. The NRL-3D Database includes standardized and frequently observed alternate names, sources, keywords, literature citations, experimental conditions and searchable sequences from model coordinates. These databases are freely accessible through the National Cancer Institute–Frederick Advanced Biomedical Computing Center at these web sites: http://www.ncifcrf.gov/RESID, http://www.ncifcrf.gov/ NRL-3D; or at these National Biomedical Research Foundation Protein Information Resource web sites: http://pir.georgetown.edu/pirwww/dbinfo/resid.html, http://pir.georgetown.edu/pirwww/dbinfo/nrl3d.html

Aplicações baseadas em geolocalizações para gestão de instalações desportivas: exemplo de utilização da API da GOOGLE Maps no concelho de Guimarães

O contexto tecnológico em que vivemos é uma realidade. E a tendência é para ser assim também no futuro. Cada vez mais. É o caso das representações de locais e entidades em mapas digitais na web. Na visão de Crocker (2014), esta tendência é ainda mais acentuada, no âmbito das aplicações móveis, como mostram as mais diversas location-based applications. No setor do desporto e da respetiva gestão nem sempre foi fácil desenvolver aplicações, recorrendo a este tipo de representações espaciais. A tecnologia não era fácil e o know-how não era adequadamente qualificado. Mas, as empresas fornecedoras de tecnologia geoespacial simplificaram o desenvolvimento de aplicações web nesta área, através da utilização de application programming interfaces (API). Como refere Svennerberg (2010), estas API’s servem de interface entre um serviço proporcionado por uma empresa, caso da Google Maps (2013) e uma aplicação web ou móvel que utiliza esses serviços. Foi com este objetivo que desenvolvemos uma aplicação web, utilizando as metodologias próprias neste domínio, como a framework de Zachman (2009), tal como foi originalmente adaptada por Whitten e Bentley (2005), onde um dos módulos é precisamente a representação de espaços desportivos, recorrendo à utilização dos serviços da Google Maps. Para além disso, toda a aplicação é suportada numa abordagem Model-View-Control (MVC). Para conseguir representar as instalações desportivas num mapa, criámos uma base de dados MySQL, com dados de longitude e latitude, de cada instalação desportiva. Através de JavaScript criou-se o mapa propriamente dito, indicando o tipo (mapa de estradas, satélite ou street view) e as respetivas opções (nível de zoom, alinhamento, controlo de interface e posicionamente, entre muitas outras opções). O passo seguinte consistiu em passar os dados para o frontend da aplicação web. Para isso, recorreu-se à integração do PHP com as livrarias externas de código JavaSrcipt, criadas especificamente para o efeito (caso da MarkerManager). A implementação destas funcionalidades permite georeferenciar todos os tipos e géneros de espaços desportivos de um concelho, região ou País. Obteve-se ainda know-how, background e massa crítica, para o desenvolvimento de novas funcionalidades. A sua utilização em dispositivos móveis é outra das possibilidades atualmente já em desenvolvimento.

Global database of surface ocean particulate organic carbon export fluxes diagnosed from the 234Th technique

Through the processes of the biological pump, carbon is exported to the deep ocean in the form of dissolved and particulate organic matter. There are several ways by which downward export fluxes can be estimated. The great attraction of the 234Th technique is that its fundamental operation allows a downward flux rate to be determined from a single water column profile of thorium coupled to an estimate of POC/234Th ratio in sinking matter. We present a database of 723 estimates of organic carbon export from the surface ocean derived from the 234Th technique. Data were collected from tables in papers published between 1985 and 2013 only. We also present sampling dates, publication dates and sampling areas. Most of the open ocean Longhurst provinces are represented by several measurements. However, the Western Pacific, the Atlantic Arctic, South Pacific and the South Indian Ocean are not well represented. There is a variety of integration depths ranging from surface to 220m. Globally the fluxes ranged from -22 to 125 mmol of C/m**2/d. We believe that this database is important for providing new global estimate of the magnitude of the biological carbon pump.