Question: How to find the mutation rate per nucleotide in aligned RNA sequences
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gravatar for npeng
7 months ago by
npeng10
npeng10 wrote:

Hi,

I am now calculating the mutation rate per nucleotide per of the aligned RNA sequences (same virus specie but different strains). I am wondering what is the common tools/programs/package/algorithms to do this calculation so that the result will be more scientific since in my raw data there is no such a reference sequence as is mentioned in literature. Any useful information about the relevant paper or tools will be highly appreciated.

Thank you!

ADD COMMENTlink modified 7 months ago by GenoMax94k • written 7 months ago by npeng10

You are aligning DNA sequence (unless you are directly sequencing RNA on nanopore), correct? What are you using to do the alignments? How do you calculate width/depth of coverage you have? How are you accounting for sequencing error (which should be small with Illumina reads but won't be zero).

ADD REPLYlink written 7 months ago by GenoMax94k

I am aligning RNA sequences. I am going to calculate the mutation rate in each nucleotide position. Thank you.

ADD REPLYlink written 7 months ago by npeng10

Where did this sequence come from? What are you aligning it to?

ADD REPLYlink written 7 months ago by GenoMax94k

Sequences come from NCBI. I used MAFFT to align them. I am seeking for help to do the next step which is to calculate the mutation rate per nucleotide.

ADD REPLYlink written 7 months ago by npeng10

A: Mutation Rates calculation
C: Mutation Rates For A Specific Gene?

ADD REPLYlink written 7 months ago by GenoMax94k

Thank you for the links. But I am trying to compute the mutation rate in each nucleotide position but not overall mutation rate. Do we have mature algorithms to do that or do I need to write my own codes to calculate that? Thank you!

ADD REPLYlink written 7 months ago by npeng10
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