Hi Jane, I believe that NCBI mouse build 36 is identical to build 36.1: http://www.ncbi.nlm.nih.gov/mapview/stats/BuildList.cgi?type=org#Musmusculus but you could contact NCBI to be sure.
This page (the "sequences" link displayed on the gateway page: http://genome.ucsc.edu/cgi-bin/hgGateway) at UCSC might also be helpful in determining whether you are looking at the same build at UCSC and NCBI: http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm8&chromInfoPage= To get around the problem of BLAT requiring 20bp sequences, you might try turning on the "Short Match" track at UCSC (in the Mapping and Sequencing Tracks section). It will display exact matches of 2-30 bases in length on the main display page of the Genome Browser (you need to actually look at each chromosome in the browser to see results). I hope this is helpful. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 07/25/11 10:18, Jane Smith wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
