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Old 01-11-2013, 09:08 AM   #1
newBioinfo
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Default V4 region primers

Hi Everyone,
I may be asking very basic question but I want to know what does 'H', 'V' and 'W' indicate in the reverse primer of V4 region of 16s rRNA. The primer sequence is GGACTACHVGGGTWTCTAAT.
Thanks!!!!
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Old 01-11-2013, 10:35 AM   #2
IonTorrent
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I believe those represent IUPAC nucleotide ambiguity codes:
http://www.bioinformatics.org/sms/iupac.html

H = A, C, or T
V = A, C, or G
W = A or T

Quote:
Originally Posted by newBioinfo View Post
Hi Everyone,
I may be asking very basic question but I want to know what does 'H', 'V' and 'W' indicate in the reverse primer of V4 region of 16s rRNA. The primer sequence is GGACTACHVGGGTWTCTAAT.
Thanks!!!!
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Old 01-11-2013, 11:10 AM   #3
newBioinfo
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Quote:
Originally Posted by IonTorrent View Post
I believe those represent IUPAC nucleotide ambiguity codes:
http://www.bioinformatics.org/sms/iupac.html

H = A, C, or T
V = A, C, or G
W = A or T
Thanks a lot!!!
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Old 01-13-2013, 11:57 PM   #4
RickBioinf
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I know that wikipedia is not the most reliable site in the world, but for this it is correct. So if you ever want to know what everything is: http://en.wikipedia.org/wiki/Nucleic_acid_sequence
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