There is one resource at HHMI here is the link

http://www.hhmi.org/biointeractive/bacterial-identification-virtual-lab

it is basically a virtual lab with PCR and capillary sequencing for bacteria identification

Hi, I frequently use FastPCR, here is the link

http://primerdigital.com/fastpcr.html

Here are a bunch of different animations, including PCR.

Don't know if I got your question right, but there is a very useful tool named "in silico PCR" developed by the bioinformatics guru Dr. Jim Kent. Take a look at: http://genome.csdb.cn/cgi-bin/hgPcr

Sebastian wrote:

"...every PCR simulation tool i found so far mainly focuses on probe match and primer design. They do not really emulate full PCR processes with all (or at least the major) potential bias and errors sources or types finally generating (hundreds of) thousand of DNA fragments."

Sebastian, in Virtual PCR (https://www.researchgate.net/publication/213744795_Genomic_PCR_simulation_with_hardware-accelerated_approximate_sequence_matching and https://www.researchgate.net/publication/12094037_Virtual_PCR) I simulated PCR cycles with amplification efficiency in individual cycles dependent on Tm of both primers and the simulated annealing temperature. I was thinking about resolving nested primers and overlaps, but never got to do that. The results were quite satisfactory, for multiplex PCR I could partially predict the ranking of individual bands in terms of band intensity. I have not followed the field closely enough for some time since, but never came across any other simulations of what might happen to important primer/template/amplicon populations in individual PCR cycles.

Conference Paper Genomic PCR Simulation With Hardware-Accelerated Approximate...

Article Virtual PCR

Just finished reading the GRINDER paper, thanks for mentioning it. Since it already simulates chimeras and you said you only missed some options for chimeras, the best thing would be to modify GRINDER (open-source) source code to suit your needs.

I use FastPCR to simulate amplifications and to test the quality of primers.

Thank so far for all answers, but still the tools mentioned are not what I'm searching for. The way they offer 'PCR simulation' is only by extracting the targeted sequence fragments (individually!) out of the reference. So they predict probable PCR products and offer a bunch of statistics about potential mismatch locations, primer efficiency, and so on but they do not imitate a PCR process.

The only exception here might be Virtual PCR, but, Matej, the link provided is a dead end (http://www.sci.muni.cz/LMFR/vpcr.html) and therefore i rejected this tool already even before you mentioned it. Maybe you cad direct me the the correct location where to download this?

Hi Sebastian. The code is now only available as an additional dataset under both papers (https://www.researchgate.net/publication/257650663_vpcr-2.1.tar). However, VPCR is not a standalone application, rather a set of programs and scripts that have to be installed and configured under a running web server. Additionally, either BLAST or PRIMEX have to be installed to support sequence matching needs. I kept it alive for 4 or 5 years since 2001 at a *.cz (version 1.0) and later *.it (version 2.0) URL. Eventually lost interest and let my own installations die. It is not an out-of-the-box thing by any standards, so I am not sure if you can easily install it on your own. A small number of users managed to install it without any help from me, so that's good. Nowadays, when programs eating 4GB of memory and 2 running threads do not overtake my entire computer, I could reinstall it here if needed. Still, from what you wrote, I doubt it can answer your rather specific needs without further modifications. For your information, the simulation in Virtual PCR really boils down to a prescribed number of cycles executing the following line in C/C++ (to be found in vpcr-do_pcr.cc):

amplicon[j] = amplicon[j] + PCR_EFFICIENCY*f_min*amplicon[j];

f_min is the fraction of amplicons/template DNA occupied by the less "sticky" primer - depends on Temp. The reaction stops when the sum of amplicons in the mix exceeds available polymerase or after the prescribed number of cycles. This allows some amplicons to outcompete others as well as prevent amplification of some of them above the "visible" threshold. There are some additional calculations that accompany this core, of course, but they do not change the simple fact that amplicons compete and accumulate exponentially until a limit is reached. To do what you need, this cycle would have to be rewritten, I am afraid.

Data vpcr-2.1.tar

Thanks Matej. I will take a deeper look into that and see if it fits or can be easily adopted to my needs. I keep you updated about any progress i make or any problems i run into if you like.

Hi Sebastian, ecoPCR is a frequently used tool for in silico PCR.

http://www.biomedcentral.com/1471-2164/11/434

http://www.grenoble.prabi.fr/trac/ecoPCR

hth Bettina

Bettina - i appreciate your helpfulness but ecoPCR is - as i have already emphasized - quite exactly the tool I'm not searching for. While it's capable of estimating barcode primer quality, barcode coverage and barcode specificity it's nevertheless far far away of emulating a PCR process.

For any other subsequent answer, i have the feeling i must redefine the situation in a different way: Let's assume i have already a 100% perfect set of primers, so there is no need to do any further primer optimization neither in vitro nor in silico. But the question now is what is the full spectrum of potential PCR products after e.g. 30 PCR cycles (and not only after one cycle)? And is there already a tool available which can perform such simulations?

Hi Sebastian, to simulate PCRs I'm using the program AmplifX. It does not simulate how your PCR products develop with increasing cycle numbers. But you can play with the cut-off values for the primer-target hybridization. Therewith you can chage the sensitivity with that primers and template match. Maybe it serves you to get an idea about what is possible after only a few cycles (using stringent conditions) or after many cycles (using weak stringency).

Another program that I used before is Amplify3. It is similar to AmplifX, but only available for Mac and it only works until Mac OS 10.6.8.