GC Skew

[Zeynep Çalıcı]

Hello  everyone

I hope your vacation is going well. I know our lessons are over, but I want to consult you about something. I hope it's okay with that.
How do we decide the window size when drawing a GC skew graph? In a genome where I've tried many window sizes, I still can't see any specific and sharp transitions. Do you have any ideas?

Sincerely 

[Dr. Andrés Aravena]

What I do is this:

Let's say that you have the genome as a vector of char, as we did in class. Then I create a new_vector with one number for each nucleotide. I use 1 for G, -1 for C, and 0 for A and T. I do like this

nucl_to_number <- c(A=0, C=-1, G=1, T=0)

new_vector <- nucl_to_number[genome]

Here new_vector and genome have the same length. This is in practice a window of size 1. We will not see anything here. Instead, I plot

cumsum(new_vector)

and I look for the minimum and maximum.

What do you think?

[Zeynep Çalıcı]

I think it's a great idea.  I will definitely apply this. 

However in some archaea there may be more than one replication origin.  Can this also be used to find the replication origin number?  Is finding only one minimum and one maximum point sufficient to find the number of replication origin? 

5 Tem 2021 Pzt 12:50 tarihinde Dr. Andrés Aravena <andres....@istanbul.edu.tr> şunu yazdı:

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[Andres Aravena]

On Mon, 5 Jul 2021 at 13:21, Zeynep Çalıcı <zeynepca...@gmail.com> wrote:

I think it's a great idea.  I will definitely apply this. 

However in some archaea there may be more than one replication origin.  Can this also be used to find the replication origin number?  Is finding only one minimum and one maximum point sufficient to find the number of replication origin? 

Good question. I know this technique for bacteria, and I know archaea have many replication origins. I'm not sure if this works on archaea, but it may be worth trying.

Notice that just min or max GC-skew is not enough. Only one is the origin, and this plot does not tell you which one. For that you can check, for example:

• if the AT content is high in that region. Low GC content helps splitting the double helix.
• which genes are close to the putative replication point. Sometimes DnaA is close

hope it helps

A

[Zeynep Çalıcı]

I took notes of what you said. Thank you so much!

Sincerely

Andres Aravena <andres....@istanbul.edu.tr>, 5 Tem 2021 Pzt, 13:50 tarihinde şunu yazdı:

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[Buse Özden]

I believe specifying local maxima and minima could be the solution in the case of archaea. The plot of the cumulative sum would display multiple local extrema along with absolute extrema since archaea have many replication origins. I found a function called extrema that returns local extrema. Maybe that would be useful for your case. 

Hope this helps. Best

5 Temmuz 2021 Pazartesi tarihinde saat 13:56:50 UTC+3 itibarıyla S.Zeynep Çalıcı şunları yazdı:

[Zeynep Çalıcı]

When I plot a graph of the sum, I see too many maximum and minimum points.  I doubt they are all have replication origins. I don't think they are all replication origins. Moreover, it goes from negative to positive or from positive to negative at many points in the skew graphic.  

I thought there some correlation with the window size.  I tried many different sizes.  However again I couldn't see any specific transition.  

I'll look into the function you mentioned. 

Thank you very much!

5 Tem 2021 Pzt 15:04 tarihinde Buse Özden <buse....@ogr.iu.edu.tr> şunu yazdı:

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