Sounds like a motif mapping problem. Maybe not the right list to post. Anyway, for motif mapping, you need - a PWM/PFM (position weight matrix/ position frequency matrix) for your element, which may be downloaded from Transfac/Jaspar/UniPROBE..... - Fetch the genomic sequence of interests (in your case, I presume 'ahead' means upstream/promoter of your gene of interest. UCSC table browser can do the job) - Pick a motif mapping program to do the search, like MEME, TFFind....
Hope this helps, Yuan On 28 Feb 2012, at 21:50, Cao, Wenlei wrote: > Hi-, All, > > We would like to know if our genes interested has a hormonal > response element ahead of the gene sequence. > > > The DNA sequence of the glucocorticoid response element is > > 5' AGAACAnnnTGTTCT 3' > > 3' TCTTGTnnnACAAGA 5' > > where n represents any nucleotide. > > Does anyone know any good way to search either using blat or any > other tools? > > You help is highly appreciated. > > Best regards, > > Wenlei > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
