Answers.Body: <p>The basic equation for PCR kinetics (Equation 1) states that the amount of amplicon after c cycles (Nc) is the starting concentration of the amplicon (N0) times the amplification efficiency (E) to the power c. The PCR efficiency in this equation is a number between 1 and 2 (2 indicates 100% efficiency). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665230/" rel="nofollow noreferrer" > NCBI </a></p>
  
  <p>In this <a href="https://www.researchgate.net/post/How_can_I_calculate_the_expected_size_for_amplification_pcr_product_in_a_pcr_reaction" rel="nofollow noreferrer" > article </a> on research gate they said <a href="https://inp.univ-amu.fr/en/amplifx-manage-test-and-design-your-primers-for-pcr" rel="nofollow noreferrer" > amplifx </a> was the software you were looking for to, calculate "(i.e. expected efficiency in PCR reaction)". The amplifx even mentions "Testing primers in in silico PCR".  </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-13T03:52:23.917Z
Answers.LastActivityDate: 2019-11-13T03:52:23.917Z
Answers.UserDisplayName: Michael Hearn
Body: <p>Let's say I've run the PCR and I now have a certain amount of the amplicon product. Is there any model that infers how much of it was there before the PCR started? I suspect it should be a probabilistic model (a distribution) parameters (shape) of which will strongly depend on the details of the PCR protocol and the characteristics of the amplicon...</p>
  
  <p>If not, then may be there are forward models that predict the amount of the amplified result from the initial content?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-12T14:39:19.747Z
Comments.Text: You need to know the primer efficiency for this to work, do you know that?
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-12T14:46:43.520Z
Comments.Text: @DevonRyan Assume, yes. You can assume I know everything. At this point I want to simply familiarize myself with any such model if there are any.
Comments.UserDisplayName: user75619
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-12T14:53:08.707Z
Comments.Text: Have you considered just using a qPCR calculator such as this http://nebiocalculator.neb.com./#!/qPCRGen ? The model of qPCR is pretty simple really, so there are a few of these premade.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-11-12T16:18:14.930Z
Comments.Text: This is qPCR based on CT number, it is common place to identify patient viraemia for example
Comments.UserDisplayName: M__
Tags: <pcr>
Title: In silico PCR: any models that can quantitatively predict the initial content from the end amplified result?
ThreadText: # In silico PCR: any models that can quantitatively predict the initial content from the end amplified result?
  
  (Asked by: username_0 on 2019-11-12)
  
  Let's say I've run the PCR and I now have a certain amount of the amplicon product. Is there any model that infers how much of it was there before the PCR started? I suspect it should be a probabilistic model (a distribution) parameters (shape) of which will strongly depend on the details of the PCR protocol and the characteristics of the amplicon...
  
  If not, then may be there are forward models that predict the amount of the amplified result from the initial content?
  
  **Tags:** pcr
  
  > **Comments:**
  > **username_1**: You need to know the primer efficiency for this to work, do you know that?  
  > **username_0**: @username_1 Assume, yes. You can assume I know everything. At this point I want to simply familiarize myself with any such model if there are any.  
  > **username_1**: Have you considered just using a qPCR calculator such as this http://nebiocalculator.neb.com./#!/qPCRGen ? The model of qPCR is pretty simple really, so there are a few of these premade.  
  > **username_2**: This is qPCR based on CT number, it is common place to identify patient viraemia for example  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2019-11-13. Score: 1
  
  The basic equation for PCR kinetics (Equation 1) states that the amount of amplicon after c cycles (Nc) is the starting concentration of the amplicon (N0) times the amplification efficiency (E) to the power c. The PCR efficiency in this equation is a number between 1 and 2 (2 indicates 100% efficiency).  [NCBI](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665230/)
  
  In this  [article](https://www.researchgate.net/post/How_can_I_calculate_the_expected_size_for_amplification_pcr_product_in_a_pcr_reaction)  on research gate they said  [amplifx](https://inp.univ-amu.fr/en/amplifx-manage-test-and-design-your-primers-for-pcr)  was the software you were looking for to, calculate "(i.e. expected efficiency in PCR reaction)". The amplifx even mentions "Testing primers in in silico PCR".
  
  
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