Querying the database annotations
Four search methods are available:
- 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 SNPs) 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.
- 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.
- 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.
- SQL search: It is available through an anonymous MySQL account. Follow these steps to run your SQL queries:
- Install the mysql client for MySQL 5.0 or any later version
- To log into the database run the following command from a terminal:
mysql -u anonymous -h www.selenodb.org -D selenodb -p
- Hit enter when prompted for a password
- Design your SQL query (the database schema may prove useful)
- Run your SQL query (you may not be able to save the query results in your local machine)
- Exit the database server with this command:
quit;
- 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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