promoter finding - (Feb/04/2006 )

hi,
I want to find promoter specially TATA boxes but the genes carry the bases only strting from transcription start site whileTATA is found on upstream side.How can I get the promoter of a gene then.

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Try digesting the DNA with specific enzymes, add adaptors , amplify the sequence, get the pcr produc sequenced and then do contig assembly... you will find the regulatory sequence...

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I would suggest doing this electronically to start with... assuming your organisms genome is known...

you use the information about the transcription start site to find the promoter in the genome (promoter is 5' to the TSS) pull out about 100bp to look for tata boxes (usually much closer than -100bp so this is good start) and then u can search using some programs or by hand... siteseer is one program--

HTH

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