I love when my situation changes on the fly. I'm now getting a dedicated (virtual) server. Were hoping to run isPcr or gfPcr AND Tomcat (serving up a Google Web Toolkit application) on a 2 CPU, 4 GB RAM server. xxPcr will only be serving up the human genome. This is expected to work, yes?
I'm trying to build the isPcr source tree using Cygwin. aliType.c builds correctly, but apacheLog.c fails. cc1 informs me that it is treating warnings as errors, and that at lines 92 and 119 , in function apacheAccessLogParse "error: array subscript as type 'char'". I have gcc 4.3.4. Should I be able to build this under Cygwin? Am I doing something stupid? I believe I completely followed the instruction in the isPcrSrc README. TIA, Greg ----- Original Message ----- From: "Jim Kent" <[email protected]> To: "Gregory Dougherty" <[email protected]> Cc: [email protected] Sent: Thursday, July 22, 2010 8:25:11 AM GMT -06:00 US/Canada Central Subject: Re: [Genome] Finding where Primers hit It sounds like in your usage case you'll want to go with gfPcr. On Jul 21, 2010, at 5:39 PM, Gregory Dougherty wrote: > 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
