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    Archive for August 16th, 2006

    How to compare promoter structure of several genes

    16th August 2006

    I needed to find out common transcription factor (TF) binding sites (TFBS) in the structure of the promoters of interferon-regulated genes. I tried several different approaches – starting from the simplest sequence-sequence comparisons using BLAST, ClustalW alignments, and searching each of the promoters for transcription factor binding sites – to compare and find common.

    But the easiest way was to use Genomatix’s “Gene2Promoter” tool. With it, the whole procedure is extremely simple:
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