MSA can be used to align promoter regions and highlight regions of conservation that may be indicative of transcription factor binding sites.

Quantitative Reverse-Transcription PCR is a modification of PCR in which RNA is first reverse transcribed into cDNA and this is amplified measuring the product (qPCR) in real time. It therefore allows one to analyze transcription by directly measuring the product (RNA) of a gene's transcription. If the gene is transcribed more, the starting product for PCR is larger and the corresponding volume of amplification is also larger.

Visual inspection of promoter region to identify putative binding sites based on previous knowledge