Hi Jim, Unfortunately, the nodes in the cluster I'll probably be using only have 2GB per CPU, so I'll be better off if I can partition the task into two 2GB chunks.
So, the situation is that I don't have a dedicated server. I have users who might have (at most) 20 pairs of primers that they will want to validate at once (i.e. "do these primers target my gene / region of interest?" "What's the size of the product they'll produce?" "Is there anything else they target?"). It's for a research lab at Mayo Clinic, and it MIGHT get used, at most, a couple of times a day. My reading is that while we could send our users to the UCSC In-Silico PCR Web page, we can NOT access it from our own program. Correct? Am I going to be spending minutes launching isPcr, and then seconds actually getting results? Is it possible to pre-compute the indexes, and then just load them in as necessary? Thank you, Greg ----- Original Message ----- From: "Jim Kent" <[email protected]> To: "Gregory Dougherty" <[email protected]> Cc: [email protected] Sent: Tuesday, July 20, 2010 7:45:52 PM GMT -06:00 US/Canada Central Subject: Re: [Genome] Finding where Primers hit Hi - if you are doing a lot of primers at once usually you want to use isPcr. If you want to have a server set up that will quickly align a few primers at a time use gfPcr. The memory these days is generally not a problem. I think 4 gig is enough for the whole genome for isPcr. On Jul 20, 2010, at 11:56 PM, Gregory Dougherty wrote: > 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 successful 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
