Question: How to handle 'N' in Nucleotide/Genes Sequences retrieved from NCBI GeneBank?
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gravatar for ammaraakhtar3
5 weeks ago by
ammaraakhtar30 wrote:

Some sequences retrieved from NCBI, contain letter 'N', which means that these nucleotide bases are not deciphered correctly, leaving an unidentified nucleotide. Should I replace N with any other base i.e. AGTC, assuming N can be any nucleotide, or I should exclude such sequences assuming that the sequencing done was not of good quality. If none of these, what I can do with such sequences in my dataset?

ADD COMMENTlink modified 5 weeks ago by Pierre Lindenbaum122k • written 5 weeks ago by ammaraakhtar30

context is missing. What is the purpose of those sequences ?? How To Ask Good Questions On Technical And Scientific Forums

ADD REPLYlink written 5 weeks ago by Pierre Lindenbaum122k

Most good tools will allow Ns in the sequences but it depends what you’re intending to do with them.

The one thing you almost certainly should not do, is replace them with a random nucleotide.

ADD REPLYlink written 5 weeks ago by jrj.healey13k
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