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baselookup

Find nucleotide codes, integers, names, and complements

Syntax

baselookup
baselookup('Complement', SeqNT)
baselookup('Code', CodeValue)
baselookup('Integer', IntegerValue)
baselookup('Name', NameValue)

Arguments

SeqNT

Nucleotide sequence(s) represented by one of the following:

  • String of single-letter codes from the table Nucleotide Lookup

  • Cell array of sequences

  • Two-dimensional character array of sequences

    Note:   If the input is multiple sequences, the complement for each sequence is determined independently.

CodeValue

Nucleotide letter code represented by one of the following:

  • String specifying a single-letter code representing a nucleotide. For valid single-letter codes, see the table Nucleotide Lookup.

  • Cell array of letter codes.

  • Two-dimensional character array of letter codes.

IntegerValueSingle integer representing a nucleotide. For valid integers, see the table Nucleotide Lookup.
NameValue

Nucleotide name represented by one of the following:

  • String specifying a nucleotide name. For valid nucleotide names, see the table Nucleotide Lookup.

  • Cell array of names.

  • Two-dimensional character array of names.

Description

baselookup displays a table of nucleotide codes, integers, names, and complements.

Nucleotide Lookup

CodeInteger Nucleotide Name MeaningComplement
A1Adenine AT
C2CytosineCG
G3GuanineGC
T4ThymineTA
U4UracilUA
R5PurineA or GY
Y6PyrimidineC or TR
K7KetoG or TM
M8AminoA or CK
S9Strong interaction (3 H bonds)C or GS
W10Weak interaction (2 H bonds)A or TW
B11Not AC or G or TV
D12Not CA or G or TH
H13Not GA or C or TD
V14Not T or UA or C or GB
N, X15Any nucleotideA or C or G or T or UN
-16Gap of indeterminate lengthGap-

baselookup('Complement', SeqNT) displays the complementary nucleotide sequence.

baselookup('Code', CodeValue) displays the corresponding meaning and nucleotide name. For ambiguous nucleotide codes (R, Y, K, M, S, W, B, D, H, V, N, and X), the nucleotide name is a descriptive name.

baselookup('Integer', IntegerValue) displays the corresponding letter code, meaning, and nucleotide name.

baselookup('Name', NameValue) displays the corresponding letter code, meaning, and nucleotide name or descriptive name.

Examples

  • Convert a nucleotide sequence to its complementary sequence.

    baselookup('Complement', 'TAGCTGRCCAAGGCCAAGCGAGCTTN')
    
    ans =
    
    ATCGACYGGTTCCGGTTCGCTCGAAN
  • Display the meaning and nucleotide name or descriptive name for the nucleotide codes G and Y.

    baselookup('Code', 'G')
    
    ans =
    
    G	 Guanine
    
    
    baselookup('Code', 'Y')
    
    ans =
    
    T|C	 pYrimidine
  • Display the nucleotide letter code, meaning, and nucleotide name or descriptive name for the integers 1 and 7.

    baselookup('Integer', 1)
    
    ans =
    
    A	 A - Adenine
    
    
    baselookup('Integer', 7)
    
    ans =
    
    K	 G|T - Keto
  • Display the corresponding nucleotide letter code, meaning, and name for cytosine and purine.

    baselookup('Name','cytosine') 
    
    ans =
    
    C	C - Cytosine
    
    
    baselookup('Name','purine')
    
    ans =
    
    R	G|A - puRine

See Also

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