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 at 4:46
Charles
91411043
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1
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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 at 4:46
Charles
91411043
add a comment |
up vote
1
down vote
favorite
up vote
1
down vote
favorite
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 at 4:46
Charles
91411043
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 at 4:46
Charles
91411043
asked Dec 2 at 4:46
Charles
91411043
asked Dec 2 at 4:46
Charles
91411043
asked Dec 2 at 4:46
Charles
91411043
asked Dec 2 at 4:46
Charles
91411043
91411043
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 at 6:16
Mowgli
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
6
down vote
accepted
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 at 6:16
Mowgli
1,163312
add a comment |
up vote
6
down vote
accepted
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 at 6:16
Mowgli
1,163312
add a comment |
up vote
6
down vote
accepted
up vote
6
down vote
accepted
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 at 6:16
Mowgli
1,163312
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 at 6:16
Mowgli
1,163312
answered Dec 2 at 6:16
Mowgli
1,163312
answered Dec 2 at 6:16
Mowgli
1,163312
answered Dec 2 at 6:16
Mowgli
1,163312
1,163312
add a comment |
add a comment |
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