Copy number calculator for realtime PCR
The Mass tab allows users to enter an exact calculation for the mass of the sequence based on input from another calculator. If you have sequence data in fasta format, you can either enter "DNA* molecular weight*" into your favorite search engine or use the Polynucleotide Molecular Weight Calculator available here at SciencePrimer.com
Comments
Marek (not verified)
Wed, 05/16/2012 - 00:00
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Perfect, bookmarked! Could I
Perfect, bookmarked! Could I have one for RNA as well?
ams
Tue, 06/05/2012 - 10:24
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Done
The calculator now does ds and ssDNA* and ssRNA
Lin (not verified)
Wed, 08/26/2015 - 04:16
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Error in ssRNA mass?
Hi,
Thanks for writing this calculator!
I am trying to calculate copy number for an RNA virus.
However, should the mass* not be calculated using 340g/mole instead of 660g/mole since that is the average molecular weight* of a single RNA molecule? Unless one has to consider the dsDNA* that is formed during the PCR??
Any explanation would help clear my confusion... Thanks!
ams
Sat, 08/29/2015 - 21:39
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340g/mole is used
When ssRNA is checked, the calculator uses 349 g / mole in the calculation.
Frank (not verified)
Wed, 12/09/2015 - 11:41
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For RNA, 340g/mole or 349 g/mole used?
When ssRNA is checked, should it be 340g/mole since the average MW for Ribonucleotide monophospates is actually 339.5?
ams
Wed, 12/09/2015 - 21:43
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It is 340
I must have mistyped 9 instead of 0
Annie (not verified)
Wed, 09/25/2013 - 17:33
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Thanks
Thank you ....this is so helpful.
ams
Thu, 09/26/2013 - 11:16
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You are welcome
I am glad you found it useful
Anonymous (not verified)
Sun, 11/03/2013 - 05:09
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Thanxxxxxxxxxxxxxxxxxxxxxxxxx
Thanxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Anonymous (not verified)
Thu, 12/19/2013 - 15:36
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RNA genomes
For ssRNA, Does this formula consider 2.53x10E6 g/mol as the molecular size for genomic RNA?
ams
Fri, 12/20/2013 - 05:40
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Not sure what you are asking
This calculator converts from ng to number of copies based on template length. Is this what you are trying to do?
Shaw (not verified)
Mon, 05/05/2014 - 07:27
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Microbiology
Hei,
thanks for calculator and explanation about calculation.
I have a question. Above formula can be used for known template lenght. How can we calculate absolute A solution is formed when one substance is dissolved into another. In a solution, the solute is the material present in the lesser amount. In other words it is the minor component. Contrast with solvent: the material present in a greater amount.
There are many different media into which materials are be dissolved. Commonly water is the solvent and a solute is the material dissolved in the water.
"> A solution is formed when one substance is dissolved into another. In a solution, the solute is the material present in the lesser amount. In other words it is the minor component. Contrast with solvent: the material present in a greater amount.
There are many different media into which materials are be dissolved. Commonly water is the solvent and a solute is the material dissolved in the water.
" class="lexicon-term">* copy numbers from unknown sample. For example I have gene of intrest in plasmid of known length. I can get standard curve with dilutions and get slope and y-intercept etc. i am intrested in calculating number of copies of X gene in a sample of DNA* from mixture of bacterial colines from lets say food sample or water. I do not know it is genomic or plasmid DNA?
is there any formula to get copy number in such sample by comparing it to satandard of known template lenght.
regards
shaw
archisman (not verified)
Fri, 05/23/2014 - 06:15
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RDNA
A DNA* sample of 100 molecular was amplified in a PCR instrument for 1 hour. Considering a cycle period* of 5 min in average, how many DNA molecular would you expect?
how to solve dis..>?
ams
Wed, 05/28/2014 - 11:34
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Must make some assumptions to answer
PCR is not a perfectly efficient process, so it is not possible to give an exact answer to this problem. This is why techniques such as real time PCR have been developed.
If, however, we assume that the reaction is perfectly efficient and that the number of molecules doubles each cycle, then after 12 cycles (5 minutes per cycle for an hour) you'd have roughty (2^12) x 100 copies.
siana (not verified)
Wed, 07/02/2014 - 07:39
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This is so helpful, thanks a
This is so helpful, thanks a lot!
Reham (not verified)
Fri, 07/11/2014 - 22:06
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b-globin gene copy number
Good evening... I am attempting a PCR experiment where i am measuring cell free DNA*, my gene of interest is b-globin.... Several authors used a conversion factor of 6.6 to converst concentration* to copy number..... I am confused about 6.6, any idea what that is?
Thanks alot
ams
Mon, 07/14/2014 - 07:31
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Related to the molecular mass of the bases
Reham - The mass* of a DNA* nucleotide is about 330 Da (Daltons). This makes the mass of a base-pair 660 Da. The calculator above uses 660 in the process of converting ng and bp to copy number.
I am not sure why the authors you site use 6.6 instead of 660, but I assume a factor of 100 is accounted for somewhere else in their calculations.
Click on the 'About the calculation' above for more on how this calculator works
olga (not verified)
Tue, 03/24/2015 - 10:08
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DNA copies
If I am using a qPCR and I get 1x106[] of DNA*, how can I calculate the genomic DNA in the sample if I don't know the amount of DNA nanograms. Is there a way to know that? The target is 200bp fragment to be amplified by qPCR while the whole genome of organism is 4419977bp.
Sylvia Norman (not verified)
Wed, 07/01/2015 - 13:48
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copy number calculator
Is this copies/mL or copies/uL?
ams
Thu, 07/02/2015 - 06:21
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Volume is not a factor in the calculation
Hi Norman,
This calculator takes a mass* of nucleotides* and strand length. It returns the total number of copies of the strands present in that amount of material. Concentration* depends on your sample.
if you have DNA* at a concentration of 100 ng/ul. Then putting 100 in for mass along with the strand length will tell you the number of copies in 100 ng of material. Since the starting units were per ul, the final units will still be per ul (ie copies/ul).
In other words, concentration depends on thE sample.
Hope this helps.
jasmin C (not verified)
Tue, 08/25/2015 - 00:56
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DNA strand length?
my gene of interest is 169bp in length. i have cloned it in to pgemt vector (3015bp).
for an absloute quantification experiment in qPCR, i would like to use this plasmid as template.
so while calculating the copy number , so my doubt is whether i should fill the column of 'length of DNA* strand' with 169 or 169+3015?
Mark (not verified)
Thu, 09/10/2015 - 11:38
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Based on actual sequence
How about adding a feature to input (eg copy and paste) a specific sequence for the copy number calc ?
That will provide a more accurate MW for the calculation.
ams
Fri, 09/11/2015 - 14:51
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Thank you or the suggestion
Hi Mark,
That would be a nice addition to the current calculator. I'm curious, how much error do you think is introduced into your work by the use of a constant mw value across all 4 bases?
- ams
TP (not verified)
Thu, 10/08/2015 - 13:31
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what is it?
Chanced upon this website. So what is the meaning of a copy number calculator in layman terms? I am a student and got curious.
sue (not verified)
Mon, 10/26/2015 - 01:25
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input of molecular weight
Hi,
an alternative to mark's suggestion would be a box for us to enter the mlecular weight* of the DNA* ourselves. We can obtain the data from cutting and pasting our sequences in other 3rd party programs which can more accurately calculate the mw. the difference can be up to 5-10% compared to the average mw using 650 or 660.
ams
Mon, 11/09/2015 - 07:43
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Great idea
Sue, I really like this suggestion. I will try to get this function added soon.
** Update **
The site now has a tool for determining the molecular weight of a polynucleotide based on it sequence. Within the next few weeks I will update this calculator to accept these molecular weight values for calculating copy number.
Anonymous (not verified)
Sun, 11/08/2015 - 23:47
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I have isolated the DNA* of
I have isolated the DNA* of my intersest .i dont know how to find the length of DNA. i am going to do PCR.
ams
Wed, 11/11/2015 - 08:30
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Too open ended
It is difficult to answer your quetion with the information you've provided. If you are doing a standard PCR off of genomic or plasmid DNA* you might not need to estimate the length at all.
LMC (not verified)
Wed, 11/25/2015 - 14:22
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Which genome size to choose from?
Hello,
I know the amount of total genomic DNA* my samples contained, but I want to figure out the copy number for a mitochondrial gene. Which genome length would I enter? The nuclear genome, mitochondrial, or a combination of both?
Thank you.
Anonymous (not verified)
Sun, 04/10/2016 - 22:33
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MW of a DNA* bp should be 660
MW of a DNA* bp should be 660 and not 330 as stated above. (Or 650 if desired). This is a typo above most likely.
ams
Tue, 04/12/2016 - 11:26
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660 for a base pair, 330 for a base
The MW will be 660 (or 650) for double stranded DNA*. The calculator also allows you to calculate copy number for single stranded DNA in which case it uses 330.