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Mutation Rates

Definition: site

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#1 Astilius

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Posted 13 April 2012 - 03:50 AM

Okay, I'm no evolutionary biologist but I was looking at the mutation rates of a virus I have an assay for and have found discussion of the rate in mutation rate in substitutions per site per year. This seems to be well and good but reading further what is discussed as a "site" seems to vary from author to author - some classify a region as a "site" (eg a promotor region), others funtional parts within a site (eg a TATA box), some classify genes as sites, some classify codons as "sites" and I've seen a few classifying nucleotides as sites.

Now, I want to get a firm handle on the mutation rate of this virus and it's important to know at what level this mutation rate is operating but am finding it difficult to get any sort of consistency in what is reported.

Is there a a definition of the term "site" here or do you need to understand what each author is referring to in each case?



What I'm really looking at is how likely my primers (in variable regions [don't ask]) for the detection of this virus are going to become blind to the virus through mutation. So need to view the reported mutation rate through that lens.
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#2 pito

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Posted 13 April 2012 - 01:47 PM

Okay, I'm no evolutionary biologist but I was looking at the mutation rates of a virus I have an assay for and have found discussion of the rate in mutation rate in substitutions per site per year. This seems to be well and good but reading further what is discussed as a "site" seems to vary from author to author - some classify a region as a "site" (eg a promotor region), others funtional parts within a site (eg a TATA box), some classify genes as sites, some classify codons as "sites" and I've seen a few classifying nucleotides as sites.

Now, I want to get a firm handle on the mutation rate of this virus and it's important to know at what level this mutation rate is operating but am finding it difficult to get any sort of consistency in what is reported.

Is there a a definition of the term "site" here or do you need to understand what each author is referring to in each case?



What I'm really looking at is how likely my primers (in variable regions [don't ask]) for the detection of this virus are going to become blind to the virus through mutation. So need to view the reported mutation rate through that lens.


For me a site is any nucleotide that changes.
You might think thats stupid because for example in humans we have a lot of non coding DNA and a mutation in that non coding DNA doesnt matter.. but when it comes down to a virus.. their DNA is pretty much coding for 200%

I guess it depends on the author. I guess some take in act whether a mutation means something or not...

But I am not a virologist and cant really help with the primer problem.

Edited by pito, 13 April 2012 - 01:52 PM.

If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#3 Astilius

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Posted 13 April 2012 - 03:10 PM

No, not stupid at all. For my purposes this would be perfect but I can easily see that depending on method to determine mutation rates and the entity in question (be it whole genomes or, say coding for a specific functional unit of a particular protein) you would naturally chose to report it in different ways.
That makes sense but they all seem to be reporting using the same terminology - "site".

I just need to make sure I'm not making a rookie error in this and thinking they all mean different things by "site" when there's a standard nomenclature that I am unaware of.

I am neither a evolutionary biologist nor a virologist either nor have much experience with RNA. I seem to have stumbled into an area in which I have little expertise but a fair few transferrable skills. Much is the way of these things.
To the last, I grapple with thee; from Hell's heart, I stab at thee; for hate's sake, I spit my last breath at thee.

#4 pito

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Posted 15 April 2012 - 07:39 AM

It happens often that people (mis)use terminology.
Perhaps, you should email some of the authors with questions related to why they used that kind of definition for the word site.

It could help you.

If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#5 Astilius

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Posted 15 April 2012 - 03:38 PM

It happens often that people (mis)use terminology.


How true, how true.
To the last, I grapple with thee; from Hell's heart, I stab at thee; for hate's sake, I spit my last breath at thee.

#6 science_guide

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Posted 15 August 2012 - 12:08 PM

A "site" in biology can mean several things.
First, it can mean the position of a nucleotide in a gene sequence or alignment. For example, you may have a single sequence and can see that at site 43 out of 650, there is an "A". You could also see that in a nucleotide alignment of two sequences, there is a single difference at site # 400. In the case of the alignment, the site # refers to every single nucleotide in the column of that alignment.

The other meaning for site is the more general one that you described wherein a "TATA" box is labeled as a "start site" for a gene. In thise case, the meaning is similar, you are still referring to a "position" or "site" along a gene sequence.

In short, site means a single position along a gene sequence or alignment.




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