I'm currently working on the methylation status of different promoters. Some of them are on genes on the reverse strand. To retrieve the sequence I'm currently using NCBI Entrez and the Eukarytoic Promoter Database but I'm not sure about the output, do I need to change the NCBI Entrez output to reverse compliment before doing any further analysis and does the Eukarytoic Promoter Database already take into account that its on the reverse strand?
Also then regarding the Primer Design when using Pyromark Assay Design how do I consider the reverse direction of the promoter or is it unnecessary?
Thank you very much for your help!