Difference between revisions of "Ambiguous nucleotide"

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Ambiguous nucleotides are used when the true nucleotide is unknown.  The most popular one seen with high-throughput genome sequences is "N" which represents any possible nucleotide.
 
Ambiguous nucleotides are used when the true nucleotide is unknown.  The most popular one seen with high-throughput genome sequences is "N" which represents any possible nucleotide.
  
Nucleotide Code
+
*Nucleotide Code
Adenosine A
+
*Adenosine A
Cytidine C
+
*Cytidine C
Guanine G
+
*Guanine G
Thymidine T
+
*Thymidine T
Uridine (if 'Alphabet' set to 'RNA') U
+
*Uridine (if 'Alphabet' set to 'RNA') U
Purine (A or G) R
+
*Purine (A or G) R
Pyrimidine (T or C) Y
+
*Pyrimidine (T or C) Y
Keto (G or T) K
+
*Keto (G or T) K
Amino (A or C) M
+
*Amino (A or C) M
Strong interaction (3 H bonds) (G or C) S
+
*Strong interaction (3 H bonds) (G or C) S
Weak interaction (2 H bonds) (A or T) W
+
*Weak interaction (2 H bonds) (A or T) W
Not A (C or G or T) B
+
*Not A (C or G or T) B
Not C (A or G or T) D
+
*Not C (A or G or T) D
Not G (A or C or T) H
+
*Not G (A or C or T) H
Not T or U (A or C or G) V
+
*Not T or U (A or C or G) V
'''Any nucleotide (A or C or G or T or U) N'''
+
'*''Any nucleotide (A or C or G or T or U) N'''

Revision as of 17:05, 23 June 2011

Ambiguous nucleotides are used when the true nucleotide is unknown. The most popular one seen with high-throughput genome sequences is "N" which represents any possible nucleotide.

  • Nucleotide Code
  • Adenosine A
  • Cytidine C
  • Guanine G
  • Thymidine T
  • Uridine (if 'Alphabet' set to 'RNA') U
  • Purine (A or G) R
  • Pyrimidine (T or C) Y
  • Keto (G or T) K
  • Amino (A or C) M
  • Strong interaction (3 H bonds) (G or C) S
  • Weak interaction (2 H bonds) (A or T) W
  • Not A (C or G or T) B
  • Not C (A or G or T) D
  • Not G (A or C or T) H
  • Not T or U (A or C or G) V

'*Any nucleotide (A or C or G or T or U) N'