seq2regexp

Convert sequence with ambiguous characters to regular expression

Syntax

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

Input Arguments

Seq

Either of the following:

  • Character vector or string containing 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, fastqread, getembl, getgenbank, getgenpept, or getpdb.

AlphabetValue

Character vector or 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

Output Arguments

RegExp

Character vector 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 Conversion

Nucleotide CodeNucleotideConversion
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 CodeAmino AcidConversion
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]

Examples

  1. Convert a nucleotide sequence to a regular expression.

    seq2regexp('ACWTMAN')

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

  2. Convert the same nucleotide sequence, but remove ambiguous characters from the regular expression.

    seq2regexp('ACWTMAN', 'ambiguous', false)

ans =
AC[AT]T[AC]A[ACGT]

See Also

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Introduced before R2006a

Bioinformatics Toolbox Documentation

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