With MySQL version 5 or higher, you can store GIS data and issue query over it . MySQL provides data types supporting openGIS requirements. Although MySQL does not support full spatial analysis, MBR-based support is very useful, if you want simple bounding box style query. To use this, you don't need any of additional package.
I found useful manual which covers almost everything I was looking for.
http://www.browardphp.com/mysql_manual_en/manual_Spatial_extensions_in_MySQL.html
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