How to deal with the Ns in gene sequences?

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7.5 years ago

lakshmi.bioinformatics ▴ 30

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 try any other methods to overcome this issue? Will this manipulate my results?

gene sequence • 1.7k views

ADD COMMENT • link updated 23 months ago by Ram 44k • written 7.5 years ago by lakshmi.bioinformatics ▴ 30

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I'd recommend masking these regions.

ADD REPLY • link 7.5 years ago by Ram 44k

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How to mask using Python program

ADD REPLY • link 7.5 years ago by lakshmi.bioinformatics ▴ 30

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

ADD REPLY • link 7.5 years ago by Ram 44k

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These are NGS reads?

ADD REPLY • link 7.5 years ago by st.ph.n ★ 2.7k

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These are gene sequences retrieved from Ensembl database

ADD REPLY • link 7.5 years ago by lakshmi.bioinformatics ▴ 30

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

ADD REPLY • link 7.5 years ago by st.ph.n ★ 2.7k

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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 REPLY • link 7.4 years ago by lakshmi.bioinformatics ▴ 30

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