By Niels Erik Nörlund (auth.)
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The transcript mapping approach (finding TSS by aligning full-length mRNA with their counterpart genomic sequence) described above usually achieves over 80% accuracy in promoter localization (66–68). The incompleteness of full-length transcripts and 5 end splice variants are the main reasons for the false-positive results. This will be improved by future advances in gene annotation. Second, although a PWM-based search is sensitive, it is not very specific because not every putative TFBS binds with its corresponding transcription factor in vivo and is, therefore, functionally significant.