Question: How to deal with the Ns in gene sequences?
0
gravatar for lakshmi.bioinformatics
2.5 years ago by
India
lakshmi.bioinformatics20 wrote:

I have around 30 k sequences and need to find the codon frequencies how to deal with the presence of Ns in the sequence

should i need to mask the regions or to replace with specific nucleotides or ty any other methods to overcome this issue will this manipulate my results

sequence N gene • 604 views
ADD COMMENTlink written 2.5 years ago by lakshmi.bioinformatics20

I'd recommend masking these regions.

ADD REPLYlink written 2.5 years ago by RamRS25k

How to mask using Python program

ADD REPLYlink written 2.5 years ago by lakshmi.bioinformatics20

Why use a Python program? Is this an assignment question?

ADD REPLYlink written 2.5 years ago by RamRS25k

These are NGS reads?

ADD REPLYlink written 2.5 years ago by st.ph.n2.5k

These are gene sequences retrieved from Ensembl database

ADD REPLYlink written 2.5 years ago by lakshmi.bioinformatics20

Is it fasta format then? If this is an assignment, can you use biopython?

ADD REPLYlink written 2.5 years ago by st.ph.n2.5k

Yes the sequence is in fasta format and how to mask with biopython also I need to draw a CGR how can it be done with biopython

ADD REPLYlink written 2.5 years ago by lakshmi.bioinformatics20
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