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  1. data AminoAcidS

    elynx-seq ELynx.Character.AminoAcidS

    Amino acids.

  2. module ELynx.Character.AminoAcidX

    Creation date: Thu Oct 4 18:26:35 2018. See header of Alphabet. Extended amino acid with gaps. See also https://www.bioinformatics.org/sms/iupac.html or https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry. 

    Amino Acid Code:  Three letter Code:  Amino Acid:
----------------  ------------------  -----------
A                 Ala                 Alanine
C                 Cys                 Cysteine
D                 Asp                 Aspartic Acid
E                 Glu                 Glutamic Acid
F                 Phe                 Phenylalanine
G                 Gly                 Glycine
H                 His                 Histidine
I                 Ile                 Isoleucine
K                 Lys                 Lysine
L                 Leu                 Leucine
M                 Met                 Methionine
N                 Asn                 Asparagine
P                 Pro                 Proline
Q                 Gln                 Glutamine
R                 Arg                 Arginine
S                 Ser                 Serine
T                 Thr                 Threonine
V                 Val                 Valine
W                 Trp                 Tryptophan
Y                 Tyr                 Tyrosine
----------------  ------------------  -----------
-                 Gap                 No amino acid
.                 Gap                 No amino acid

  3. data AminoAcidX

    elynx-seq ELynx.Character.AminoAcidX

    Amino acids.

  4. module ELynx.Character.Nucleotide

    Creation date: Thu Oct 4 18:26:35 2018. See header of Alphabet. 

    Symbol  Description  Bases represented  Complement
------  -----------  -----------------  ----------
A       Adenine      A                  T
C       Cytosine        C               G
G       Guanine            G            C
T       Thymine               T         A

  5. data Nucleotide

    elynx-seq ELynx.Character.Nucleotide

    Nucleotides.

  6. module ELynx.Character.NucleotideI

    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)                      -

  7. data NucleotideI

    elynx-seq ELynx.Character.NucleotideI

    NucleotideIs.

  8. module ELynx.Character.NucleotideX

    See header of Alphabet. Extended nucleotides with gaps. See also https://www.bioinformatics.org/sms/iupac.html or https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry. 

    Symbol  Description  Bases represented  Complement
------  -----------  -----------------  ----------
A       Adenine      A                  T
C       Cytosine        C               G
G       Guanine            G            C
T       Thymine               T         A
------  -----------  -----------------  ----------
- or .  Gap (Zero)                      -

  9. data NucleotideX

    elynx-seq ELynx.Character.NucleotideX

    Extended nucleotides.

  10. fieldWidth :: Int

    elynx-seq ELynx.Sequence.Defaults

    Field width for tables.

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