Difference between primary and secondary sequence database?

Primary sequence databases contain raw sequence data derived from the sequencing of genes etc. whereas secondary sequence databases contain information that is derived from primary sequence databases. For example this could be active site residues of protein families that were found by carrying out multiple sequence alignments on the raw primary sequence database data for a set of related proteins. Primary sequence databases can be nucleic databases (such as EMBL, GenBank or DDBJ) or protein databases (such as Swiss-PROT or trEMBL). An example of a secondary sequence database is PROSITE.