cbt”") for each replicon. These files contain all the required protein information and a simplified representation of the tools’ results. Some initialization files containing information about phylogeny or genome features are also used. The repository is
used by the Graphical User Interface (GUI) to display CoBaltDB information. For raw data from tools, the GUI accesses the marshal file directory. Accessing the CoBaltDB Repository and Raw Data The CoBaltDB platform has been developed as a client-server application. The server is installed at the Genouest Bioinformatics platform http://www.genouest.org/?lang=en. The client is a Java application that needs to be locally downloaded by the users. selleck products Queries are submitted to the server-side CoBaltDB repository using a locally installed client GUI that provides tabular and graphical representations of the data. The repository selleckchem is accessed through SOAP-based web services (Simple Object Access Protocol), implemented in Java 5 using the Apache Axis 1.4 toolkit
and deployed on the servlet engine Tomcat 5.5.20. CoBaltDB integrates: an initialization web service (that returns the current list of genomes supported); two repository web services that allow querying the database either by specifying a replicon or a list of locus tags; and a raw data web service that retrieves all recorded raw data generated by a given tool for the specified locus tag. Utility Running CoBaltDB Our goal was to build an open-access reference database providing access to protein localization predictions. CoBaltDB was designed to centralize different types of data and to interface them so as to help researchers rapidly Pregnenolone analyse and develop hypotheses concerning the subcellular distribution of particular protein(s) or a given proteome.
This data management allows comparative evaluation of the output of each tool and database and thus straightforward identification of inaccurate or conflicting predictions. We developed a user-friendly CoBaltDB GUI as a Java 5 client application using NetBeans 5.5.1 IDE. It presents four tabs that perform specific tasks: the “”input”" tab (Figure 2) allows selecting the organism whose proteome localizations will be presented, using organism name completion or through an alphabetical list. Alternatively, users may also enter a subset of proteins, specified by their locus tags. The “”Specialized tools”" tab (Figure 3) supplies a table showing, for each protein identified by its locus tag or protein identifier, some annotation information such as its gene name, description and links to the corresponding NCBI and KEGG web pages. Clicking on a “”locus tag”" opens a navigator window with the related KEGG link, and clicking on a “”protein Id”" opens the corresponding NCBI entry web page.