RT Journal
A1 Down, Thomas A.
A1 Hubbard, Tim J. P.
T1 Computational Detection and Location of Transcription Start Sites in Mammalian Genomic DNA
JF Genome Research 
JO Genome Research 
YR 2002 
FD March 01 
VO 12 
IS 3 
SP 458 
OP 461 
DO 10.1101/gr.216102 
UL http://genome.cshlp.org/content/12/3/458.abstract 
AB Transcription, the process whereby RNA copies are made from sections of the DNA genome, is directed by promoter regions. These define the transcription start site, and also the set of cellular conditions under which the promoter is active. At least in more complex species, it appears to be common for genes to have several different transcription start sites, which may be active under different conditions. Eukaryotic promoters are complex and fairly diffuse structures, which have proven hard to detect in silico. We show that a novel hybrid machine-learning method is able to build useful models of promoters for >50% of human transcription start sites. We estimate specificity to be >70%, and demonstrate good positional accuracy. Based on the structure of our learned models, we conclude that a signal resembling the well known TATA box, together with flanking regions of C-G enrichment, are the most important sequence-based signals marking sites of transcriptional initiation at a large class of typical promoters.