You don't use a database file, you use a database and use SQL to search it. (At least, that's the standard.) You will probably use DBI and the appropriate DBD modules to access it from your scripts.

Most small projects use MySQL as their database, though PostgreSQL is popular. For large projects, you might have access to Oracle or Sybase, and there's many others. Tiny project might be able to get away with SQLite.

More info could help, like what system you're on. If you're on Windows, SQL*Server (accessed using [DBD::Sybase) is often a good choice.