We know that the four native bases for DNA are AGTC, however, some of the sequences, retrieved from NCBI, contain letter 'N', which illustrates 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?
P.S I can't find any help in Entrez Sequences Help Catalog.
The best option is to remove the bases marked with "N", because they could not be identified, probably due to problems of DNA sequencing or poor quality of dna. However, as has been said, some programs can handle this problem.
The bases marked by N could not be identified due to the low quality of the DNA sequence.
With programs as Chromas or others you can look how the chromatogram looks like and eventually edit manually the base when is clear not ambiguous and it is
possible. Some programs can handle the Ns.
Best of luck
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