are The sequences of any gene in ncbi database that given in genbank file as DNA written as both strand ? or just one of them so how can we design primer F and R primer?
I wish to let you know that the sequences available in the GenBank are the sense sequences read in 5' to 3' orientation only. If you are using any GenBank sequences to make primers, your forward primer will have to be in the same sequence and in the same orientation as the GenBank sequence. This will bind to the anti-sense template strand and amplify downstream. On the other hand, for reverse primer you have to design reverse-complementary oligo sequence on the said GenBank Sequence. This primer will bind to the sense strand and amplify upstream. However, if you are using a primer designing software, you just have to feed the GenBank sequence (sense strand only), identify the region of interest and primer conditions. Rest of the calculations will be done by the software and optimal primer pairs will be returned.
I wish to let you know that the sequences available in the GenBank are the sense sequences read in 5' to 3' orientation only. If you are using any GenBank sequences to make primers, your forward primer will have to be in the same sequence and in the same orientation as the GenBank sequence. This will bind to the anti-sense template strand and amplify downstream. On the other hand, for reverse primer you have to design reverse-complementary oligo sequence on the said GenBank Sequence. This primer will bind to the sense strand and amplify upstream. However, if you are using a primer designing software, you just have to feed the GenBank sequence (sense strand only), identify the region of interest and primer conditions. Rest of the calculations will be done by the software and optimal primer pairs will be returned.