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The biggest problem with Tkprof is that it needs "you" to be knowledgeable enough to interpret what it reveals and that's what Oracle is trying to improve with the self-tuning components that it has introduced in the past two releases. See this thread on Asktom where Tom tells how to use Tkprof effectively and what its all about,
A somewhat old (Oracle 9i) but still valid description and comparison of Oracle command line tuning tools (EXPLAIN PLAN, AUTOTRACE, SQL trace/TKPROF, Statpsack and Tome Kyte's own tool run_stats) can be found in chapter 2 of Oracle Efficient by Design http://asktom.oracle.com/pls/apex/z?p_url=ASKTOM%2Edownload_file%3Fp_file%3D1887128923702383570&p_cat=ch02.pdf&p_company=822925097021874.
This can be the answer (quote of Tom) for my question:
to use tkprof for query tuning, you are getting half of what you need - the FACTS. The other half is all about you - and your knowledge of >the database. If you don't have or don't want to have that other half, you will be using tools such as the performance pack in enterprise manager.