Thank you Robert. Would it be possible to add a link to that on the discussion list page? https://lists.soe.ucsc.edu/mailman/listinfo/genome
Perhaps next to the link to the archives. Greg ----- Original Message ----- From: "robert kuhn" <[email protected]> To: "Jim Kent" <[email protected]> Cc: "Gregory Dougherty" <[email protected]>, [email protected] Sent: Tuesday, July 20, 2010 2:23:48 PM GMT -06:00 US/Canada Central Subject: Re: [Genome] Finding where Primers hit hello, greg, there is a page of information about searching the site, including the mailing-list archives here: http://genome.ucsc.edu/contacts.html sorry it wasn't easier to find! best wishes, --b0b kuhn ucsc genome bioinformatics group On 7/20/2010 11:52 AM, Jim Kent wrote: > Please use In Silico PCR, which was designed just for this purpose. > > On Jul 20, 2010, at 4:51 PM, Gregory Dougherty wrote: > >> Hi all, >> >> I hope this isn't a FAQ, I couldn't find any way to search the archives. >> >> I am writing a program that takes pairs of PCR Primer sequences, and returns >> the products they will produce when used w/ human DNA. My first thought was >> to use BLAT to figure out where the primers match the genome. While this >> has worked well with test primers that are 20+ bases long, BLAT won't run on >> smaller Primers, and my users have Primers as small as 18 bases. >> >> Is BLAT a reasonable tool to use for solving this problem? If we download >> the source, change the 20 base limit to 18, and then run that BLAT, will >> that work? Work only if the sequence is a perfect match? Fail miserably? >> >> May be OT: Can I get Blast to tell me WHERE the primer hit in the item it >> hit in? "Homo sapiens chromosome 17 genomic contig, GRCh37 reference >> primary assembly, Length=21169982" really isn't a very useful hit report. >> >> Thanks in advance, >> >> Greg >> _______________________________________________ >> 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
