Thanks, that does look as if it will do what I want. ----- Original Message ----- From: "Jim Kent" <[email protected]> To: "Gregory Dougherty" <[email protected]> Cc: "genome" <[email protected]> Sent: Wednesday, August 4, 2010 3:37:06 PM GMT -06:00 US/Canada Central Subject: Re: [Genome] Segmentation Fault running gfServer
I see - if you're looking for primer cross-hybe in any serious way, the in-silico PCR tools are just not the right ones for the job. Greg Schuler's ePCR would be a better starting point. On Aug 4, 2010, at 1:10 PM, Gregory Dougherty wrote: > I'm validating already created primers. One of the things I'm doing is > telling the users if their primers will target anything else in the genome. > Since a 20 base primer with, oh, an A to T mismatch at position 10 is still > going to bind quite adequately, I need to be able to find those situations > before they bite my users. (IOW, one of the main purposes of the program I'm > working on is to warn the users when their primer pair is also going to bind > and amplify someplace else. For that I need to find less than perfect > matches.) > > Other than setting MACHTYPE to x86_64, is there anything I need to do to make > sure it all compiles 64 bit? > > Thanks, > > Greg > > ----- Original Message ----- > From: "Jim Kent" <[email protected]> > To: "Gregory Dougherty" <[email protected]> > Cc: "genome" <[email protected]> > Sent: Wednesday, August 4, 2010 2:57:33 PM GMT -06:00 US/Canada Central > Subject: Re: [Genome] Segmentation Fault running gfServer > > Try it on a larger machine, and make sure you're runing a version compiled > with 64 bit. > > You are pushing the envelope here Greg. > > _Why_ do you need to have less of the 3' end match perfectly? Are you > amplifying non-human DNA with human primers? > > On Aug 4, 2010, at 10:19 AM, Gregory Dougherty wrote: > >> On a server w/ 8 GB of RAM I tried running gfServer with a stepSize of 1, >> tileSize of 11, on hg18. I got a Segmentation Fault. Running it with >> stepSize of 2 works, and on a 4GB machine the stepSize of 2 generates a "not >> enough memory" error rather than a segfault. >> >> Is this a known problem? The machine is x86_64, running Linux. >> >> TIA, >> >> 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
