MySQL will choose the appropriate index for the tables involved in your query; in my experience it chooses correctly most of the time. I see from another post in this thread that your query is:
select topic FROM table1 WHERE uri LIKE '$q'
You can find out what indexes are used by MySQL in this query by running the command
EXPLAIN SELECT topic FROM table1 WHERE uri LIKE 'something'
where "something" is one of your parameters. You can see what indexes are defined on your table by running the command
SHOW CREATE TABLE table1;