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'
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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'
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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;
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