A method of searching a document having nested-structure document-specific markup (such as Extensible Markup Language (XML)) involves 112 receiving a query that designates at least (A) a phrase to be matched in a phrase matching process, and (B) a selective designation of at least a tag or annotation that is to be ignored during the phrase matching process. The method further involves 114 deriving query-specific indices based on query-independent indices that were created specific to each document, and 116 carrying out the phrase matching process using the query-specific indices on the document having the nested-structure document-specific markup.