What do you mean by other letters aside from A, C, G, and T in DNA sequencing r - (Nov/24/2006 )
I am sequencing the 16s rDNA encoding gene of by bacterial isolates. I did my first sequencing experiment yesterday using the primers 10f, 530f, 800 r and 1401 r. I am expecting A, C, G and T in my sequences but I found other letters such as M, W, S, Y, R, and others. There are many of these letter at the beginning and at the end of my sequence. I can also find some at the middle of the sequence. MAy I know what do these letters imply? Does each letter has its meaning or I just delete them... Thank you
Symbol: nucleotide(s)
A adenine
C cytosine
G guanine
T thymine in DNA;
uracil in RNA
U deoxy-Uracil in DNA;
uracil in RNA
I inosine
N A or C or G or T
M A or C
R A or G
W A or T
S C or G
Y C or T
K G or T
V A or C or G; not T
H A or C or T; not G
D A or G or T; not C
B C or G or T; not A
Thank you so much Kersten for a very helpful reply.
May I also ask why these characters coding for a certain nucleotide appear in the sequence? If we will paste the sequence containing these characters in the BLAST search these will definitely affect the result. You mean there is a need to substitute the possible combination?
May I also ask why these characters coding for a certain nucleotide appear in the sequence? If we will paste the sequence containing these characters in the BLAST search these will definitely affect the result. You mean there is a need to substitute the possible combination?
You should be able to cut and paste. The other letters are approved by the IUPAC and were added to the basic four to maintain the single-letter-for-a-single-base code, so that even if a sequence showed polymorphisms, it could still be analysed by computer. Imagine how much more difficult it would be to wade through lots of "A/T" or "A/C/G" sequences...