A method and system for cleansing anomalies from sequence-based data at query time. Sequence-based data such as RFID data is loaded into a database. One or more cleansing rules are received at a cleansing rules engine. The cleansing rule engine converts the cleansing rule(s) to a template that includes logic to compensate for anomalies in the sequence-based data. A query to retrieve the sequence-based data is received by a query rewrite engine. The query rewrite engine rewrites the query by applying the template logic. The rewritten query is executed at query time. The result of the rewritten query execution is identical to the result of executing the original query on a data set generated by applying the cleansing rule to all of the sequence-based data.