Thank you Hiram and Jim for pointing me in the right direction. Looking at the code, for my situation I have two workable choices: gfPcr or isPcr.
Questions: 1: Is gfPcr actually a workable choice? I.E. will it let me search for hits from 18 base primers, and will it be as successfull as isPcr at finding hits? 2: The ReadMe says that isPcr "builds its own index". Is it creating it's own index, or loaded an already calculated one from files? 3; For isPcr, roughly how much is "a lot of memory"? In particular, roughly how much space does it take from Chr1, and roughly how much does it take for the whole human genome? Thanks again, Greg ----- Original Message ----- From: "Jim Kent" <[email protected]> To: "Gregory Dougherty" <[email protected]> Cc: [email protected] Sent: Tuesday, July 20, 2010 1:52:22 PM GMT -06:00 US/Canada Central Subject: Re: [Genome] Finding where Primers hit 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
