Whole Grain Flour

 You can substitiute whole grain for white flour. Whole grain flours usually take more liquid.  You won't achive simmilar results. I used to adapt recipes this way. It helped me to learn how to creat my own recipes. Now I bake only whole grain breads and I love their flavor.

You can see my sourdough whole grain bagels here :

http://bochenkowo.blogspot.com/2011/05/sourdough-buckwheat-bagels.html

http://bochenkowo.blogspot.com/2010/09/bagels-and-twists.html

http://bochenkowo.blogspot.com/2009/11/bajgle-zytnio-pszenne.html

I have made two starters. One from whole wheat flour

and another one  from whole rye flour. 

 I made them following the instruction from: WHOLE GRAIN BAKING  The King Arthur Flour Company. I think that Peter Reinhart's Whole Grain Bread would be helpful for you.