Hi Heather, Please see this thread from our mailing list archives: https://lists.soe.ucsc.edu/pipermail/genome/2008-August/017035.html
Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Heather Miller wrote, On 11/10/10 13:00: > Hi, > I have another question regarding the Table Browser. I know how to obtain > sequence from a batch of entries. Obtaining additional upstream sequence is > also not a problem. However, now I want to obtain promoter regions that are > 2100 bp before and 2050 bp after the transcription start site of each gene. > How can I do this? I have 66 genes to look at. > > Thanks, > Heather Miller > > Heather Miller, PhD > Teaching Associate > North Carolina State University > Biotechnology Education Facility > 6105 Jordan Hall > Box 7512 > Raleigh, NC 27695 > [email protected] > (919) 513-7685 > www.ncsu.edu/biotechnology > >>>> Brooke Rhead <[email protected]> 10/25/10 8:15 PM >>> >>>> > Hi Heather, > > The Table Browser can do batch queries. First select the gene track you > are using from the drop-down menus, then click the "identifiers > (names/accessions): paste list" button and enter your list of genes. > When you get sequence as output, it will be for all of the genes in your > list (in FASTA format). > > If you have further questions, please feel free to contact us again at > [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > On 10/23/10 09:37, Heather Miller wrote: > >> Hi, >> I'm am trying to obtain sequence of promoter regions of a large list >> > of genes (~150). I can grab sequence for each individual gene (2000 bp > up and downstream of the first exon) by using the Table Browser, but I > would like to see if there is a way to do this as a batch. > >> Thanks, >> Heather Miller >> >> Heather Miller, PhD >> Teaching Associate >> North Carolina State University >> Biotechnology Education Facility >> 6105 Jordan Hall >> Box 7512 >> Raleigh, NC 27695 >> [email protected] >> (919) 513-7685 >> www.ncsu.edu/biotechnology >> >> _______________________________________________ >> 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
