seq2regexp - Convert sequence with ambiguous characters to regular expression

Syntax

Input 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, fastqread, 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

Output Arguments

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]

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

regexp | regexpi | restrict | seqwordcount

© 1984-2012- The MathWorks, Inc.    -   Site Help   -   Patents   -   Trademarks   -   Privacy Policy   -   Preventing Piracy   -   RSS