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:
You can find out what indexes are used by MySQL in this query by running the commandselect topic FROM table1 WHERE uri LIKE '$q'
where "something" is one of your parameters. You can see what indexes are defined on your table by running the commandEXPLAIN SELECT topic FROM table1 WHERE uri LIKE 'something'
SHOW CREATE TABLE table1;