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
