Hello,
I was looking for S/MAR sequences in the promoter regions of some genes. I used Emboss SMARScan and Genomatix SMARTest. I entered the same sequences in both the tools but the outputs of possible MARs were different. The two tools showed different regions as S/MARs. How can I be sure which one is the true S/MAR?
Hi Apoorva,
are the identified portions totally different? Is not there any overlapping portions? It the two algorithms are different there may be some difference among the outputs. You may use the overlapping regions to call high confident results....
The regions predicted by the two sites are not overlapping.. Some are proximal to each other while some are very distant.
Unfortunately, until you validate them biochemically you can't be sure either is true (in your cell type). Remember these tools are predictors and may have variable sensitivity and specificity. I recommend looking up a qPCR validation similar to that used by Keaton et al. (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017912).
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