Good Morning Greg: There is a program in the kent source tree for this purpose: isPcr It is part of the blat suite of programs. A zip file of the source: http://genome-test.cse.ucsc.edu/~kent/src/isPcr33.zip or in the source tree itself: http://genome-test.cse.ucsc.edu/~kent/src/unzipped/isPcr/ http://genomewiki.ucsc.edu/index.php/Getting_Started_With_Git#Genome_Browser_Mirror_Sites
--Hiram ----- Original Message ----- From: "Gregory Dougherty" <[email protected]> To: [email protected] Sent: Tuesday, July 20, 2010 7:51:48 AM GMT -08:00 US/Canada Pacific Subject: [Genome] Finding where Primers hit 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
