elynx-seq-0.7.2.2: Handle molecular sequences
Copyright2021 Dominik Schrempf
LicenseGPL-3.0-or-later
Maintainerdominik.schrempf@gmail.com
Stabilityunstable
Portabilityportable
Safe HaskellSafe-Inferred
LanguageHaskell2010

ELynx.Character.NucleotideI

Description

Creation date: Thu Oct 4 18:26:35 2018.

See header of Alphabet.

Nucleotide IUPAC code. See also https://www.bioinformatics.org/sms/iupac.html or https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry.

Remarks:

  • Question marks (?) are interpreted as unknowns (same as N). However, when a sequence is printed/exported, Ns will be used.
  • Full stops (.) are interpreted as gaps (same as -). However, when a sequence is printed/exported, -s will be used
Symbol  Description  Bases represented  Complement
------  -----------  -----------------  ----------
A       Adenine      A                  T
C       Cytosine        C               G
G       Guanine            G            C
T       Thymine               T         A
------  -----------  -----------------  ----------
U       Uracil                U         A
W       Weak         A        T         W
S       Strong          C  G            S
M       aMino        A  C               K
K       Keto               G  T         M
R       puRine       A     G            Y
Y       pYrimidine      C     T         R
B       not A           C  G  T         V
D       not C        A     G  T         H
H       not G        A  C     T         D
V       not T        A  C  G            B
------  -----------  -----------------  ----------
N       any          A  C  G  T         N           (preferred)
?       any          A  C  G  T         N
------  -----------  -----------------  ----------
-       Gap (Zero)                      -           (preferred)
.       Gap (Zero)                      -
Synopsis

Documentation

data NucleotideI Source #

NucleotideIs.

Constructors

A 
C 
G 
T 
U 
W 
S 
M 
K 
R 
Y 
B 
D 
H 
V 
N 
Gap 

Instances

Instances details
Bounded NucleotideI Source # 
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Enum NucleotideI Source # 
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Read NucleotideI Source # 
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Show NucleotideI Source # 
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Character NucleotideI Source # 
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CharacterI NucleotideI Source # 
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CharacterX NucleotideI Source # 
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Eq NucleotideI Source # 
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Ord NucleotideI Source # 
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Unbox NucleotideI Source # 
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Vector Vector NucleotideI Source # 
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MVector MVector NucleotideI Source # 
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newtype Vector NucleotideI Source # 
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newtype MVector s NucleotideI Source # 
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Defined in ELynx.Character.NucleotideI