The database manager

Concept

The database manager manage genome files and stores them according to a pre defined structure on the harddrive. There is also a built in ftp client which can download genomes from a ftp server, e.g. NCBI, directly to the Gegenees database.

The Database manager

To open the database manager, in the menu bar click "Data" -> "Database manager". A "default" database is always present but customized databases can also be made. The default database represents a directory called "database" in the workspace directory. Custom databases represent directories named "database_NameOfCustomDatabase". If the database is large, subsets can be shown by entering a case sensitive filter text. (e.g Bacillus to show only the genus Bacillus). There is also a filter for showing only genomes in draft or complete form. Initially the database is empty. To add genomes, eihter import them form the file system or use the build in ftp client to download files from a ftp server.

 

Importing genomes

Import from file system

There are currently two supported file formats; Fasta files (e.g. ".fna") and Genbank files (".gbk"). It is possible to import several genomes at once, as long as each genome is in a separate directory. To import a genome from the file system, in the database manager click "Data" -> "Import from Filesystem". Then select in the combo box what kind of format you are importing. Then select the directory to import from by clicking the "..."-button. Now, Gegenees extract some info from the genomes that are imported. If the number of genomes to import is very high (1000+) this might take a few minutes. Then select if the genomes you are importing are draft genomes or complete genomes and click ok.

Import from file system

 

Import from remote file system

To import a genome through the ftp client, in the database manager click "Data" -> "Import by FTP". Then in the site combo box, select a ftp server to connect to and click the refresh button below. Its the one with two yellow arrows on. To download a genome to the local database, select the genome and click on the right arrow button.

Content table If a remote genome is already in the local database, it will be colored red in the remote list.