Hi Jane, I'm glad to hear the Short Match track was useful!
A couple of extra notes on your problem from our engineers: - NCBI build 36.1 refers to assembly 36, annotation #1. NCBI increments the version number when they update their *annotations* of the assembly, but the assembly itself is left unchanged. So build 36, 36.1, 36.2, etc., would all be based on the same underlying assembly. - If you are comfortable running unix command-line tools, the oligoMatch tool in the source tree (available here: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads) can also be used to find perfect sequence matches. The assembly .2bit files for mouse are available here: http://hgdownload.cse.ucsc.edu/downloads.html#mouse (under the "Full data set" links). -- Brooke Rhead UCSC Genome Bioinformatics Group On 07/25/11 19:38, Brooke Rhead wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
