Is there a program out there that can quickly tell you what the 5' region of a given gene is?
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Posted 19 February 2009 - 07:43 PM
There is no program that can tell you which sequence is a promoter by just looking at a piece of sequence. promoter predction must consider many other parameters. Although there are promoter prediction programs they only have a limited success in predicting promoters. With the availbility of genome data, espeically expression data such as ESTs and mRNAs, finding promoter sequences is no longer a formidable task as it was many years ago. By just browsing genome database such as UCSC and Enseml, we are very confident that a sequence immediately upstream of a transcript is a promoter sequence especially if there is a CpG island in the sequence. I think transcription data provides the best prediction of a promoter sequence.