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.

IntegerValue Single 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

Code	Integer	Nucleotide 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	`A` or `G`	`Y`
`Y`	`6`	Pyrimidine	`C` or `T`	`R`
`K`	`7`	Keto	`G` or `T`	`M`
`M`	`8`	Amino	`A` or `C`	`K`
`S`	`9`	Strong interaction (3 H bonds)	`C` or `G`	`S`
`W`	`10`	Weak interaction (2 H bonds)	`A` or `T`	`W`
`B`	`11`	Not `A`	`C` or `G` or `T`	`V`
`D`	`12`	Not `C`	`A` or `G` or `T`	`H`
`H`	`13`	Not `G`	`A` or `C` or `T`	`D`
`V`	`14`	Not `T` or `U`	`A` or `C` or `G`	`B`
`N`, `X`	`15`	Any nucleotide	`A` or `C` or `G` or `T` or `U`	`N`
`-`	`16`	Gap of indeterminate length	Gap	`-`

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

baselookup - Find nucleotide codes, integers, names, and complements

Syntax

Arguments

Description

Examples

See Also

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