rtree: know your nearest neigbhors
My computer spends a lot of time looking for neighbors of a given location-- even more so for bio, than for geo. This is what I've learned about the options for doing smarter search so far. SELECT * from ( (SELECT * FROM ((SELECT * FROM feature WHERE start<= ? ORDER BY start DESC LIMIT 1) UNION (SELECT * FROM feature where start>= ? ORDER BY start LIMIT 1)) as u) UNION (SELECT * FROM ((SELECT * FROM feature where stop<= ? ORDER BY stop DESC LIMIT 1) UNION (SELECT * FROM feature where stop>= ? ORDER BY stop LIMIT 1)) as v) ) as w ORDER BY ABS((start + stop)/2 - ?) LIMIT 1 if you fill in ? with an integer location, that query will return the closest feature most of the time. It's verbose if not ugly, and that's only for 1 dimension. It can return the wrong feature in certain cases.... You have to write it like that in MySQL, because it doesnt support functional indexes , so as soon as you do something like: ORDER BY ABS((start + stop)/2 - ?) it's no lon