Question: Chaos game representation application using Biopython
0
gravatar for lakshmi.bioinformatics
2.5 years ago by
India
lakshmi.bioinformatics20 wrote:

I have a bunch of gene sequences for which I need to draw the chaos game representation model how can I do this using Biopython also I have Ns in the sequence how to mask them

ADD COMMENTlink written 2.5 years ago by lakshmi.bioinformatics20
1

That should really be multiple sentences. I have no idea what you are asking. Can you please rephrase it in more detail, and with correct grammar?

ADD REPLYlink written 2.5 years ago by Brian Bushnell17k

I need to prepare a chaos game representation(CGR) model for around 30k gene sequences in the gene sequences there are lot of places marked with Ns(hope you know what are Ns) this is the work my doubt is can I prepare CGR using Biopython if yes how to deal with the Ns in the sequences

ADD REPLYlink written 2.5 years ago by lakshmi.bioinformatics20

Hint: use . , ; ! ?

ADD REPLYlink written 2.5 years ago by h.mon28k

hope you know what are Ns

Another hint: don't be rude with people trying to help you.

ADD REPLYlink written 2.5 years ago by h.mon28k

sorry @h.mon I was not trying to be rude since I was asked to explain my question I was doing it since I guessed the term N is well known I mentioned it in this fashion.

Sorry if I ment to be hurting someone

ADD REPLYlink written 2.5 years ago by lakshmi.bioinformatics20

Thank you for pointing it out @h.mon I shall avoid these kind of statements in future

ADD REPLYlink written 2.5 years ago by lakshmi.bioinformatics20

This web tool allows the visualization of DNA sequence in CGR: https://codepen.io/alojzije/full/xfmKr. Though this is not the answer, this may help you. Look also at the code give in this page: https://petridishtalk.com/2012/02/27/chaos-game-analysis-of-genomes/

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by cpad011212k

thank you @ cpad0112

ADD REPLYlink written 2.5 years ago by lakshmi.bioinformatics20
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