| Bioinformatics Toolbox™ | |
SeqChar = int2nt(SeqInt)
SeqChar = int2nt(SeqInt,
...'Alphabet', AlphabetValue, ...)
SeqChar = int2nt(SeqInt,
...'Unknown', UnknownValue, ...)
SeqChar = int2nt(SeqInt,
...'Case', CaseValue, ...)
| SeqInt | Row vector of integers specifying a nucleotide sequence. For valid integers, see the table Mapping Nucleotide Integers to Letter Codes. Integers are arbitrarily assigned to IUB/IUPAC letters. |
| AlphabetValue | String specifying a nucleotide alphabet. Choices are:
|
| UnknownValue | Character to represent unknown nucleotides, that is 0 or integers ≥ 17. Choices are any character other than the nucleotide characters A, C, G, T, and U and the ambiguous nucleotide characters N, R, Y, K, M, S, W, B, D, H, and V. Default is *. |
| CaseValue | String specifying the case of the returned character string. Choices are 'upper' (default) or 'lower'. |
| SeqChar | Nucleotide sequence specified by a character string of codes. |
SeqChar = int2nt(SeqInt) converts SeqInt, a row vector of integers specifying a nucleotide sequence, to SeqChar, a string of codes specifying the same nucleotide sequence. For valid codes, see the table Mapping Nucleotide Integers to Letter Codes.
Mapping Nucleotide Integers to Letter Codes
| Nucleotide | Integer | Code |
|---|---|---|
| Adenosine | 1 | A |
| Cytidine | 2 | C |
| Guanine | 3 | G |
| Thymidine | 4 | T |
| Uridine (if 'Alphabet' set to 'RNA') | 4 | U |
| Purine (A or G) | 5 | R |
| Pyrimidine (T or C) | 6 | Y |
| Keto (G or T) | 7 | K |
| Amino (A or C) | 8 | M |
| Strong interaction (3 H bonds) (G or C) | 9 | S |
| Weak interaction (2 H bonds) (A or T) | 10 | W |
| Not A (C or G or T) | 11 | B |
| Not C (A or G or T) | 12 | D |
| Not G (A or C or T) | 13 | H |
| Not T or U (A or C or G) | 14 | V |
| Any nucleotide (A or C or G or T or U) | 15 | N |
| Gap of indeterminate length | 16 | - |
| Unknown (any integer not in table) | 0 or ≥ 17 | * (default) |
SeqChar = int2nt(SeqInt, ...PropertyName', PropertyValue, ...) calls int2nt with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:
SeqChar = int2nt(SeqInt,
...'Alphabet', AlphabetValue, ...) specifies
a nucleotide alphabet. AlphabetValue can be 'DNA',
which uses the symbols A, C, G,
and T, or 'RNA', which uses the symbols A, C, G,
and U. Default is 'DNA'.
SeqChar = int2nt(SeqInt, ...'Unknown', UnknownValue, ...) specifies the character to represent unknown nucleotides, that is 0 or integers ≥ 17. UnknownValue can be any character other than the nucleotide characters A, C, G, T, and U and the ambiguous nucleotide characters N, R, Y, K, M, S, W, B, D, H, and V. Default is *.
SeqChar = int2nt(SeqInt, ...'Case', CaseValue, ...) specifies the case of the returned character string. CaseValue can be 'upper' (default) or 'lower'.
Convert a nucleotide sequence from integer to letter representation.
s = int2nt([1 2 4 3 2 4 1 3 2]) s = ACTGCTAGC
Convert a nucleotide sequence from integer to letter representation and define # as the symbol for unknown numbers 17 and greater.
si = [1 2 4 20 2 4 40 3 2]; s = int2nt(si, 'unknown', '#') s = ACT#CT#GC
Bioinformatics Toolbox™ functions: aa2int, baselookup, int2aa, nt2int
| int2aa | isoelectric | |
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