How can i reveals sequence features correlated with recombination rate

Question

[mostafarafiepour]

Hi all

I want to know how and with what methods and software i can reveals sequence features correlated with recombination rate??

for example:

the results clearly showed a strong positive correlation between recombination rate and GC-rich sequences and a negative correlation with AT-rich sequences.

So, i want to know this is done using what software or script?

Best Regard

Mostafa

[Benn]

This is probably done with functions like cor() in R. However, your quote doesn't tell which correlation was used (Pearson is mostly used, but Spearman's rank is also common).

If you want a more specific answer, I suggest you explain with what kind of data you are working, or from which paper you quote.

[mostafarafiepour]

Hi, many thanks for your reply,

my data is whole genome sequencing and as i said before, i want to find sequence features correlated with recombination rate.

My pattern article was sent in the attachment:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661806/pdf/510.pdf

[Benn]

What have you tried so far? In the methods of the paper (last two paragraphs) they describe what they have done. This is a whole study what you're asking here, not just a simple script. You can't expect members of Biostars here to write these scripts for you. Ask a local bioinformatician for help if this is too much for you, or try to collaborate with the authors of the paper.

[mostafarafiepour]

Yes, As you well said, in the last two paragraphs of the paper, the method was mentioned. But there is nothing to see how this analysis is done? As you mentioned need a script, unfortunately, the author of the article did not mention them. And in fact I'm looking for these scripts. And I do not know how to design them?

[Joe]

It appears they also used a modified version of the CRI-MAP software. It should be considered poor academic form if this software is not made available with the published article.

I would contact the paper corresponding author. If you do not get a response, I would be inclined to complain to the journal that the software and scripts are not made available (which in my opinion should be grounds for retraction if they refuse).

[mostafarafiepour]

Hi, i agree with your opinion and i think the best way is to first contact the paper corresponding author.

Can you contact the paper corresponding author?

[Joe]

I can't - but you can. Just get their email from the paper. They should have provided one. If you know their name (from the paper) and their institution, you can always look up their information online.

Answer 1

[Joe]

Maybe you're interested in something like ClonalFrameML or Gubbins?

I think FastGear and BRAT-NextGen are options too.

They essentially look for signatures of recombination in phylogenetic data, but the usecases are quite particular (whole genomes typically), so it depends what you're doing precisely.

[mostafarafiepour]

Hi,

my data is whole genome sequencing. Please see the attached article (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661806/pdf/510.pdf). My goal is to do something exactly like this article. But unfortunately, this article does not mention the way it worked.