If I understand correctly, you want to define a specific color in an image file to be transparent. I don’t know if this is possible in Blender. My suggestion is to use an image processing program like Photoshop or GIMP and select the portions of your image that are the target color and erase them. Then save as a .png file which will preserve the alpha channel.
Then the recipe that I use in Blender is:
- Game Menu> Blender GLSL Materials
- Materials>Render pipeline: ZTransp
- Materials: Alpha = 0
- Materials>Texture: UV and Flat
- Materials>Texture>Map To: Col and Alpha
- Texture>Image: Premul
- Texture>Map Image: Use Alpha