Connecting from Microsoft to DB2 is easy, you should install ODBC driver (for example Client Access ODBC driver) or ado provider (for example Client Access) this allows direct connection from SQL server to DB2 on iSeries.
Connecting from DB2 to Microsoft SQL is more difficult since the SQL server doesn't support DRDA and the iSeries connect verb uses DRDA. JDBC is an option, yet it requires you to write your application on the iSeries in Java so the best you could do is use a product described very well here by Kent Milligan He answers in detail the issue of iSeries to other databases issue.
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This was first published in October 2002