What would “N” and “V” stand for in DNA barcoding?
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I'm currently looking protocol for PAT-seq, and when it talks about the barcoding that's utilized, the documentation mentions there being an "N" and "NN" in the sequence, as well as a "V". For example:
...CCGATCTNNxxxTTT...TTTVN
where the "..." is an abbreviation of the the sequence and the "xxx" is the location of the barcode sequence.
As you can see, there's an "NN" just before the barcode sequence, and then, at the end of the T sequence there's a "VN". It says that the "NN" serves to affirm that the reads obtained are derived from different RT reactions and not all from a single RT product that's been excessively amplified.
So, I'm guessing that the "N" just stands for an undetermined nucleotide. Is that right? But then, what about the "V"?
molecular-biology experimental-design barcoding
asked Dec 2 '18 at 4:46
CharlesCharles
92411043
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add a comment |
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I'm currently looking protocol for PAT-seq, and when it talks about the barcoding that's utilized, the documentation mentions there being an "N" and "NN" in the sequence, as well as a "V". For example:
...CCGATCTNNxxxTTT...TTTVN
where the "..." is an abbreviation of the the sequence and the "xxx" is the location of the barcode sequence.
As you can see, there's an "NN" just before the barcode sequence, and then, at the end of the T sequence there's a "VN". It says that the "NN" serves to affirm that the reads obtained are derived from different RT reactions and not all from a single RT product that's been excessively amplified.
So, I'm guessing that the "N" just stands for an undetermined nucleotide. Is that right? But then, what about the "V"?
molecular-biology experimental-design barcoding
asked Dec 2 '18 at 4:46
CharlesCharles
92411043
$endgroup$
add a comment |
$begingroup$
I'm currently looking protocol for PAT-seq, and when it talks about the barcoding that's utilized, the documentation mentions there being an "N" and "NN" in the sequence, as well as a "V". For example:
...CCGATCTNNxxxTTT...TTTVN
where the "..." is an abbreviation of the the sequence and the "xxx" is the location of the barcode sequence.
As you can see, there's an "NN" just before the barcode sequence, and then, at the end of the T sequence there's a "VN". It says that the "NN" serves to affirm that the reads obtained are derived from different RT reactions and not all from a single RT product that's been excessively amplified.
So, I'm guessing that the "N" just stands for an undetermined nucleotide. Is that right? But then, what about the "V"?
molecular-biology experimental-design barcoding
asked Dec 2 '18 at 4:46
CharlesCharles
92411043
$endgroup$
I'm currently looking protocol for PAT-seq, and when it talks about the barcoding that's utilized, the documentation mentions there being an "N" and "NN" in the sequence, as well as a "V". For example:
...CCGATCTNNxxxTTT...TTTVN
where the "..." is an abbreviation of the the sequence and the "xxx" is the location of the barcode sequence.
As you can see, there's an "NN" just before the barcode sequence, and then, at the end of the T sequence there's a "VN". It says that the "NN" serves to affirm that the reads obtained are derived from different RT reactions and not all from a single RT product that's been excessively amplified.
So, I'm guessing that the "N" just stands for an undetermined nucleotide. Is that right? But then, what about the "V"?
molecular-biology experimental-design barcoding
molecular-biology experimental-design barcoding
asked Dec 2 '18 at 4:46
CharlesCharles
92411043
asked Dec 2 '18 at 4:46
CharlesCharles
92411043
asked Dec 2 '18 at 4:46
CharlesCharles
92411043
asked Dec 2 '18 at 4:46
CharlesCharles
92411043
asked Dec 2 '18 at 4:46
CharlesCharles
92411043
92411043
add a comment |
add a comment |
1 Answer
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It is standard IUPAC nomenclature to write bases that are not uniquely defined.
For example, "N" means "any base", but "V" means "A, C or G, but not T".
See the full list here
answered Dec 2 '18 at 6:16
MowgliMowgli
1,265313
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1 Answer
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1 Answer
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$begingroup$
It is standard IUPAC nomenclature to write bases that are not uniquely defined.
For example, "N" means "any base", but "V" means "A, C or G, but not T".
See the full list here
answered Dec 2 '18 at 6:16
MowgliMowgli
1,265313
$endgroup$
add a comment |
$begingroup$
It is standard IUPAC nomenclature to write bases that are not uniquely defined.
For example, "N" means "any base", but "V" means "A, C or G, but not T".
See the full list here
answered Dec 2 '18 at 6:16
MowgliMowgli
1,265313
$endgroup$
add a comment |
$begingroup$
It is standard IUPAC nomenclature to write bases that are not uniquely defined.
For example, "N" means "any base", but "V" means "A, C or G, but not T".
See the full list here
answered Dec 2 '18 at 6:16
MowgliMowgli
1,265313
$endgroup$
It is standard IUPAC nomenclature to write bases that are not uniquely defined.
For example, "N" means "any base", but "V" means "A, C or G, but not T".
See the full list here
answered Dec 2 '18 at 6:16
MowgliMowgli
1,265313
answered Dec 2 '18 at 6:16
MowgliMowgli
1,265313
answered Dec 2 '18 at 6:16
MowgliMowgli
1,265313
answered Dec 2 '18 at 6:16
MowgliMowgli
1,265313
1,265313
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add a comment |
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