Genome-wide search models. A: Search model created by Trinklein. The gene location coordinates do not specify the location coordinates of different transcripts. B: Modified search model. This search model uses unique transcript location coordinates instead of unique gene location coordinates. Based on this modified search model, the intergenic region between the third transcript (T3) of gene 1 and the transcript of gene 2 can be considered to be a BD PRO. Such promoters would not be detected by the previous search model because the TSS of the first transcript (T1) of gene 1 would be considered the 5′-most boundary of the gene1 location coordinates that overlap with gene 2.