Sequence input for bisulfite PCR primer design - (Dec/08/2004 )

I want to design primers for bisulfite sequencing PCR. I don't know if the direction of the sequence matters ( I mean that I can enter either + stand or - stand, which is the complement sequcence).

Yes, the direction of the input sequence matters.

For bisulfite PCR, after DNA modification, two strands are no longer complementary, most programs will only take the input sequence as it is and design primers on it. If you are interested in mapping the antisense strand, you have to complment and invert the sense strand before feed into the program.