palindromes - Find palindromes in sequence

Syntax

Arguments

SeqNT	One of the following: String of codes specifying a nucleotide sequence. For valid letter codes, see the table Mapping Nucleotide Letter Codes to Integers. Row vector of integers specifying a nucleotide sequence. For valid integers, see the table Mapping Nucleotide Integers to Letter Codes. MATLAB structure containing a Sequence field that contains a nucleotide sequence, such as returned by emblread, fastaread, fastqread, genbankread, getembl, or getgenbank.
LengthValue	Integer specifying a minimum length for palindromes. Default is 6.
ComplementValue	Controls the return of complementary palindromes, that is, where the elements match their complementary pairs A-T (or U) and C-G instead of an exact nucleotide match. Choices are true or false (default).

Description

[Position, Length] = palindromes(SeqNT) finds all palindromes in sequence SeqNT with a length greater than or equal to 6, and returns the starting indices, Position, and the lengths of the palindromes, Length.

[Position, Length, Pal] = palindromes(SeqNT) also returns a cell array, Pal, of the palindromes.

... = palindromes(SeqNT, ...'PropertyName', PropertyValue, ...) calls palindromes 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:

... = palindromes(SeqNT, ..., 'Length', LengthValue, ...) finds all palindromes longer than or equal to LengthValue. Default is 6.

... = palindromes(SeqNT, ..., 'Complement', ComplementValue, ...) controls the return of complementary palindromes, that is, where the elements match their complementary pairs A-T (or A-U) and C-G instead of an exact nucleotide match. Choices for ComplementValue are true or false (default).

Examples

Find the palindromes in a simple nucleotide sequence.

[p,l,s] = palindromes('GCTAGTAACGTATATATAAT')

p =
    11
    12
l =
     7
     7
s = 
    'TATATAT'
    'ATATATA'

Find the complementary palindromes in a simple nucleotide sequence.

[pc,lc,sc] = palindromes('TAGCTTGTCACTGAGGCCA',...
                         'Complement',true)
pc =
     8
lc =
     7
sc = 
    'TCACTGA'

Find the palindromes in a random nucleotide sequence.

a = randseq(100)

a =
TAGCTTCATCGTTGACTTCTACTAA
AAGCAAGCTCCTGAGTAGCTGGCCA
AGCGAGCTTGCTTGTGCCCGGCTGC
GGCGGTTGTATCCTGAATACGCCAT

[pos,len,pal]=palindromes(a)

pos =
    74
len =
     6
pal = 
    'GCGGCG' 

See Also

regexp | seqcomplement | seqrcomplement | seqreverse | seqshowwords | strfind

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