Hi, I am interested in finding a short DNA binding element (12bp) within the mouse genome. I can submit via NCBI blastn a 16 letter sequence and find a large number of putative binding sites. I want to find these same sites on the mouse genome browser to pull down the DNA sequence and make primers. But the coordinates are different. I saw somewhere that there was a converter but I'm not sure how to use it. It would be so so much easier if the two websites had at least ONE build in common!!! NCBI has a choice of 36.1. The genome browser has only even assemblies, 35, 36 and 37. I've tried to contact NCBI about having plain 36 but the person answering my question did not know what I was talking about.
I have tried to get around the problem using blat, but it requires 20bp sequences and only pulls exact scores and does not give me as much useful information as I can get with blastn. Please help. Thanks, Jane _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
