For such a general query, you could try reading the documentation:
http://www.cs.waikato.ac.nz/~ml/weka/index.html
See also various tutorials such as
http://maya.cs.depaul.edu/~classes/ect584/WEKA/associate.html
Any more details would require a more specific question.
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Please modify your question with specific details on "bioinformatics application" for better answers. You may also check the R package arules as an alternate for Weka for association mining
Are you looking for suggestions to understand how effective is WEKA for finding association rules for a bioinformatics problem ? Please provide specific details for better answers.