Finding sequence conservation

I have written about sequence conservation in vertebrates previously but without much elaboration, hence I'm writing another post on this topic. An assumption of sequence conservation is that regions that show conservation, are under purifying selection, i.e. alleles that decrease the fitness of an organism are removed, and therefore probably do something important. Protein-coding regions...

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Transcription factor binding site prediction

Updated 2013 December 17th to include JASPAR I have a simple task: given a short DNA sequence and I want to know if there are any potential transcription factor binding sites within this sequence. I looked online and found this transcription factor binding site prediction tool called TFSEARCH. It's very straight-forward; all you have to...

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Position weight matrix

The process of transcription, is influenced by the interaction of proteins called transcription factors (TFs) that bind to specific sites called Transcription Factor Binding Sites (TFBSs), which are proximal or distal to a transcription starting site. TFs generally have distinct binding preferences towards specific TFBSs, however TFs can tolerate variations in the target TFBS. Thus...

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Transcription factor binding site analysis

Updated 2013 October 4th. Recently I've been looking into transcription factor binding site analyses. With my mind set on this, I thought I'll brush up this old post. MEME is a tool for discovering motifs in a group of related DNA or protein sequences. As a discovery tool, it is able to find de novo...

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