| Bioinformatics Toolbox | |
Display nucleotide codes, integers, names, and abbreviations
baselookup
baselookup('Complement', SeqNT)
baselookup('Code', CodeValue)
baselookup('Integer', IntegerValue)
baselookup('Name', )
SeqNT | Nucleotide sequence. Enter a character string of single-letter codes from the Nucleotide Lookup Table below. In addition to a single nucleotide sequence, SeqNT can be a cell array of sequences, or a two-dimensional character array of sequences. The complement for each sequence is determined independently |
Code | Nucleotide letter code. Enter a single character from the Nucleotide Lookup Table below. Code can also be a cell array or a two-dimensional character array. |
Nucleotide integer. Enter an integer from the Nucleotide Lookup Table below. Integers are arbitrarily assigned to IUB/IUPAC letters. | |
Name | Nucleotide name. Enter a nucleotide name from the Nucleotide Lookup Table below. NameValue can also be a single name, a cell array, or a two-dimensional character array. |
Nucleotide Lookup Table
| Code | Integer | Base Name | Meaning | Complement |
|---|---|---|---|---|
A | 1 | Adenine | A | T |
C | 2 | Cytosine | C | G |
G | 3 | Guanine | G | C |
T | 4 | Thymine | T | A |
| U | 4 | Uracil | U | A |
R | 5 | (PuRine) | G|A | Y |
Y | 6 | (PYrimidine) | T|C | R |
K | 7 | (Keto) | G|T | M |
M | 8 | (AMino) | A|C | K |
S | 9 | Strong interaction (3 H bonds) | G|C | S |
W | 10 | Weak interaction (2 H bonds) | A|T | W |
B | 11 | Not-A (B follows A) | G|T|C | V |
D | 12 | Not-C (D follows C) | G|A|T | H |
H | 13 | Not-G (H follows G) | A|T|C | D |
V | 14 | Not-T (or U) (V follows U) | G|A|C | B |
N,X | 15 | ANy nucleotide | G|A|T|C | N |
- | 16 | Gap of indeterminate length | Gap | - |
baselookup displays a table of all nucleotide codes, integers, meanings, and names.
baselookup('Complement', SeqNT) displays the complementary nucleotide sequence.
baselookup('Code', CodeValue) displays the corresponding letter code, meaning, and name. For ambiguous nucleotide letters (R Y K M S W B D H V N X), the name is replace by a descriptive name.
displays the corresponding letter code, meaning, and nucleotide name.
baselookup('Name', NameValue) displays the corresponding letter code and meaning.
baselookup('COMPLEMENT', 'TAGCTGRCCAAGGCCAAGCGAGCTTN')
baselookup('name','cytosine')
Bioinformatics Toolbox functions aminolookup, basecount, codoncount, dimercount, geneticcode, nt2aa, nt2int, revgeneticcode
| | basecount | biograph (biograph) | |
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