Bioinformatics Toolbox™

seq2regexp - Convert sequence with ambiguous characters to regular expression

Syntax

RegExp = seq2regexp(Seq) RegExp = seq2regexp(Seq, ...'Alphabet', AlphabetValue, ...) RegExp = seq2regexp(Seq, ...'Ambiguous', AmbiguousValue, ...)

Arguments

Seq

Either of the following:

Character string of codes specifying an amino acid or nucleotide sequence.
Structure containing a Sequence field that contains an amino acid or nucleotide sequence, such as returned by fastaread, getembl, getgenbank, getgenpept, or getpdb.

AlphabetValue

String specifying the sequence alphabet. Choices are:

'NT' (default) — Nucleotide
'AA' — Amino acid

AmbiguousValue

Controls whether ambiguous characters are included in RegExp, the regular expression return value. Choices are:

true (default) — Include ambiguous characters in the return value
false — Return only unambiguous characters

Return Values

RegExp

Character string of codes specifying an amino acid or nucleotide sequence in regular expression format using IUB/IUPAC codes.

Description

RegExp = seq2regexp(Seq) converts ambiguous amino acid or nucleotide symbols in a sequence to a regular expression format using IUB/IUPAC codes.

RegExp = seq2regexp(Seq, ...'PropertyName', PropertyValue, ...) calls seq2regexp 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:

RegExp = seq2regexp(Seq, ...'Alphabet', AlphabetValue, ...) specifies the sequence alphabet. AlphabetValue can be either 'NT' for nucleotide sequences or 'AA' for amino acid sequences. Default is 'NT'.

RegExp = seq2regexp(Seq, ...'Ambiguous', AmbiguousValue, ...) controls whether ambiguous characters are included in RegExp, the regular expression return value. Choices are true (default) or false. For example:

If Seq = 'ACGTK', and AmbiguousValue is true , the MATLAB^® software returns ACGT[GTK] with the unambiguous characters G and T and the ambiguous character K.
If Seq = 'ACGTK', and AmbiguousValue is false, the MATLAB software returns ACGT[GT] with only the unambiguous characters.

Nucleotide Conversions

Nucleotide Code	Nucleotide	Conversion
`A`	Adenosine	`A`
`C`	Cytosine	`C`
`G`	Guanine	`G`
`T`	Thymidine	`T`
`U`	Uridine	`U`
`R`	Purine	`[AG]`
`Y`	Pyrimidine	`[TC]`
`K`	Keto	`[GT]`
`M`	Amino	`[AC]`
`S`	Strong interaction (3 H bonds)	`[GC]`
`W`	Weak interaction (2 H bonds)	`[AT]`
`B`	Not `A`	`[CGT]`
`D`	Not `C`	`[AGT]`
`H`	Not `G`	`[ACT]`
`V`	Not `T` or `U`	`[ACG]`
`N`	Any nucleotide	`[ACGT]`
`-`	Gap of indeterminate length	`-`
`?`	Unknown	`?`

Amino Acid Conversion

Amino Acid Code	Amino Acid	Conversion
`B`	Asparagine or Aspartic acid (Aspartate)	`[DN]`
`Z`	Glutamine or Glutamic acid (Glutamate)	`[EQ]`
`X`	Any amino acid	`[A R N D C Q E G H I L K M F P S T W Y V]`

Example

Convert a nucleotide sequence into a regular expression.

seq2regexp('ACWTMAN')

ans =
AC[ATW]T[ACM]A[ACGTRYKMSWBDHVN]