findPalindromes {Biostrings} | R Documentation

## Searching a sequence for palindromes

### Description

The `findPalindromes` function can be used to find palindromic regions in a sequence.

`palindromeArmLength`, `palindromeLeftArm`, and `palindromeRightArm` are utility functions for operating on palindromic sequences. They should typically be used on the output of `findPalindromes`.

### Usage

    findPalindromes(subject, min.armlength=4,
                    max.looplength=1, min.looplength=0, max.mismatch=0,
                    allow.wobble=FALSE)

    palindromeArmLength(x, max.mismatch=0, allow.wobble=FALSE)
    palindromeLeftArm(x, max.mismatch=0, allow.wobble=FALSE)
    palindromeRightArm(x, max.mismatch=0, allow.wobble=FALSE)

### Arguments

`subject` | An XString object containing the subject string, or an XStringViews object.
`min.armlength` | An integer giving the minimum length of the arms of the palindromes to search for.
`max.looplength` | An integer giving the maximum length of "the loop" (i.e the sequence separating the 2 arms) of the palindromes to search for. Note that by default (`max.looplength=1`), `findPalindromes` will search for strict palindromes only.
`min.looplength` | An integer giving the minimum length of "the loop" of the palindromes to search for.
`max.mismatch` | The maximum number of mismatching letters allowed between the 2 arms of the palindromes to search for.
`allow.wobble` | Logical indicating whether wobble base pairs (G/U or G/T base pairings) should be treated as mismatches (the default) or matches.
`x` | An XString object containing a 2-arm palindrome, or an XStringViews object containing a set of 2-arm palindromes.

### Details

The `findPalindromes` function finds palindromic substrings in a subject string. The palindromes that can be searched for are either strict palindromes or 2-arm palindromes (the former being a particular case of the latter) i.e. palindromes where the 2 arms are separated by an arbitrary sequence called "the loop".

If the subject string is a nucleotide sequence (i.e. DNA or RNA), the 2 arms must contain sequences that are reverse complement from each other. Otherwise, they must contain sequences that are the same.

### Value

`findPalindromes` returns an XStringViews object containing all palindromes found in `subject` (one view per palindromic substring found).

`palindromeArmLength` returns the arm length (integer) of the 2-arm palindrome `x`. It will raise an error if `x` has no arms. Note that any sequence could be considered a 2-arm palindrome if we were OK with arms of length 0 but we are not: `x` must have arms of length greater or equal to 1 in order to be considered a 2-arm palindrome. When applied to an XStringViews object `x`, `palindromeArmLength` behaves in a vectorized fashion by returning an integer vector of the same length as `x`.

`palindromeLeftArm` returns an object of the same class as the original object `x` and containing the left arm of `x`.

`palindromeRightArm` does the same as `palindromeLeftArm` but on the right arm of `x`.

Like `palindromeArmLength`, both `palindromeLeftArm` and `palindromeRightArm` will raise an error if `x` has no arms. Also, when applied to an XStringViews object `x`, both behave in a vectorized fashion by returning an XStringViews object of the same length as `x`.

### Author(s)

H. Pagès, with contributions from Erik Wright and Thomas McCarthy

### See Also

`maskMotif`, `matchPattern`, `matchLRPatterns`, `matchProbePair`, XStringViews-class, DNAString-class

### Examples

    x0 <- BString("abbbaabbcbbaccacabbbccbcaabbabacca")

    pals0a <- findPalindromes(x0, min.armlength=3, max.looplength=5)
    pals0a
    palindromeArmLength(pals0a)
    palindromeLeftArm(pals0a)
    palindromeRightArm(pals0a)

    pals0b <- findPalindromes(x0, min.armlength=9, max.looplength=5,
                              max.mismatch=3)
    pals0b
    palindromeArmLength(pals0b, max.mismatch=3)
    palindromeLeftArm(pals0b, max.mismatch=3)
    palindromeRightArm(pals0b, max.mismatch=3)

    ## Whitespaces matter:
    x1 <- BString("Delia saw I was aileD")
    palindromeArmLength(x1)
    palindromeLeftArm(x1)
    palindromeRightArm(x1)

    x2 <- BString("was it a car or a cat I saw")
    palindromeArmLength(x2)
    palindromeLeftArm(x2)
    palindromeRightArm(x2)

    ## On a DNA or RNA sequence:
    x3 <- DNAString("CCGAAAACCATGATGGTTGCCAG")
    findPalindromes(x3)
    findPalindromes(RNAString(x3))

    ## Note that palindromes can be nested:
    x4 <- DNAString("ACGTTNAACGTCCAAAATTTTCCACGTTNAACGT")
    findPalindromes(x4, max.looplength=19)

    ## Treat wobble base pairings as matches:
    x5 <- RNAString("AUGUCUNNNNAGGCGU")
    findPalindromes(x5, max.looplength=4, min.looplength=4)
    findPalindromes(x5, max.looplength=4, min.looplength=4, max.mismatch=2)
    findPalindromes(x5, max.looplength=4, min.looplength=4, allow.wobble=TRUE)

    ## A real use case:
    library(BSgenome.Dmelanogaster.UCSC.dm3)
    chrX <- Dmelanogaster$chrX
    chrX_pals0 <- findPalindromes(chrX, min.armlength=40, max.looplength=80)
    chrX_pals0
    palindromeArmLength(chrX_pals0)  # 251 70 262

    ## Allowing up to 2 mismatches between the 2 arms:
    chrX_pals2 <- findPalindromes(chrX, min.armlength=40, max.looplength=80,
                                  max.mismatch=2)
    chrX_pals2
    palindromeArmLength(chrX_pals2, max.mismatch=2)  # 254 77 44 48 40 264

[Package Biostrings version 2.60.2 Index]