Public Sigenae Contig Browser .

Information Software Ensj Ensj Quick Start

1. Install ensj-XX-Y.jar and mysql-*.jar in your classpath.
2. Get a driver connected to an ensembl database. e.g.
   • Use the default registry to get a driver for the latest human core database on ensembldb.ensembl.org (requires no user configuration):

     import org.ensembl.driver.CoreDriver;
     import org.ensembl.registry.Registry;
     ...
     Registry registry = Registry.createDefaultRegistry();
     CoreDriver coreDriver = registry.getGroup("human").getCoreDriver();
     

   • Use a configuration file to specify the database (the database_prefix parameter means "use the latest human core database"):

     CoreDriver coreDriver = CoreDriverFactory.createCoreDriver("my_database.properties");
     ...
     
     #my_database.properties:
     host ensembldb.ensembl.org
     port 3306
     user anonymous
     database_prefix homo_sapiens_core
     

   • Use a factory method to specify the database:

     CoreDriver coreDriver =
     CoreDriverFactory.createCoreDriver("ensembldb.ensembl.org",
     3306, "homo_sapiens_core_25_34e", "anonymous", null);
     

3. Use an adaptor from the driver to retrieve data of interest. e.g.

   
   List genes = coreDriver.getGeneAdaptor().fetch(new Location("chromosome:2:20m-21m:1"))
   for (int j = 0; j < genes.size(); j++) {
     Gene g = (Gene) genes.get(j);
     System.out.println(g.getAccessionID());
   }
   

© 2012 INRA / WTSI / EBI.