Predicting transcriptional start site (tss) for sigma 70 promoter - (Apr/14/2008 )
I needed to predict the transcriptional start site (TSS) for a sigma 70 promoter in e.coli and am looking for a good web tool for this. I don’t need to identify lots of putative promoters in a genome (as is usually the case for these tools); rather I need to predict which specific base is the TSS for a promoter that is already known to initiate transcription. Does anyone know of a good tool for this? Or have any recommendations for good models in the literature? I can make a guess by hand based on papers like this one:
Hawley DK and McClure WR. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res 1983 Apr 25; 11(8) 2237-55. pmid:6344016.
But was wondering if there is a tool available.
I don't think there is a tool. Preferentially it will start on a purine (G or A) around 5-7 bp downstream from the TATAAT -10 sequence.