why nucleotides is more than 4?

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huda nawaf
huda nawaf 2011-11-16
hi as I know the no. of nucleotides is 4 letters. why in matlab consider it 17 letters as in table here:
http://www.mathworks.com/help/toolbox/bioinfo/ref/int2nt.html
thanks

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Walter Roberson
Walter Roberson 2011-11-16
The table there looks pretty straight-forward to me: http://www.mathworks.com/help/toolbox/bioinfo/ref/int2nt.html#bp_rekb-1 . It has codes for situations in which particular sets of nucleotides are known to be present or known to be absent.
Besides, the number of known nucleotides is not 4: it is currently 8. The 7th and 8th were announced in July 2011, with the 5th and 6th having been announced in April 2005.
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huda nawaf
huda nawaf 2011-11-16
Thanks,
but currently, we have to deal with just four because when convert necleotides into aminoacid we have to use this table:
http://www.mathworks.com/help/toolbox/bioinfo/ref/nt2aa.html
or may in new ver. of matlab deal with new nucleotides.

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Lucio Cetto
Lucio Cetto 2011-11-19
Ambiguous nucleotide symbols are used to characterize sequences that can have variations. It was introduced in the 80's and they are useful nowadays in certain cases, for example describing restriction enzymes. (e.g. http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html). In my personal opinion I think that there are other situations in which we have better options, such as sequence motifs, sequence profiles and the more elaborated profile HMMs. If you plan to convert to aa, Matlab can actually use also ambiguous aa codes when possible, although this is no longer a standard practice; most people now uses only ACGT.

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