SelenoDB
Release 1.0

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Querying the database annotations

Four search methods are available:

  1. Simple keyword search: It is available, for convenience, at the top of each page in the site. It is a quick and easy way to search all or specific feature reports (sequence, gene, promoter, transcript, protein, SECIS and others) with a single keyword. No keyword will search and match all feature reports in the database and produce a list ordered first by species phylogeny, then alphabetically by family and subfamily name.

  2. Simple species/family search: It is available, for convenience, at the bottom of each page in the site. It provides a fast link to Gene reports for species selenoproteomes or selenoprotein families across species. By default (All species and All families), it will provide a list of all Gene reports ordered first by species phylogeny and then alphabetically by family and subfamily name.

  3. Advanced search: It is available, for convenience, as a link at the top and bottom right of each page in the site under the name Advanced. It merges the two previous types of searches in a flexible and powerful searching schema that allows to query the feature reports by groups of common features. No selection will match all feature reports in the database and report a list of features ordered first by species phylogeny and then alphabetically by gene name.

  4. Graphical search: It is available, for convenience, as a link at the top and bottom left of each page in the site under the name Chart. It is an integrated view of the annotated selenoproteomes by species and family in the database. Whole families or species together with single genes can be queried with a simple mouse click. The data is displayed in such a way to emphasize the dynamics of Sec/Cys usage throughout species and families. It will result in a list of gene reports for the selected species or gene famliy.

  5. SQL search: It is available through an anonymous MySQL account. Follow these steps to run your SQL queries:
    1. Install the mysql client for MySQL 5.0 or any later version
    2. To log into the database run the following command from a terminal:
      mysql -u anonymous -h www.selenodb.org -D selenodb -p
      
    3. Hit enter when prompted for a password
    4. Design your SQL query (the database schema may prove useful)
    5. Run your SQL query (you may not be able to save the query results in your local machine)
    6. Exit the database server with this command:
      quit;
      
    7. To save the query results in a local file run the same SQL query directly from the terminal:
      mysql -u anonymous -h www.selenodb.org -D selenodb -p -e "your query here" -N > your_local_file
      

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