R: Find Patterns in DNA Sequences

where {ape} | R Documentation

## Find Patterns in DNA Sequences

### Description

This function finds patterns in a single or a set of DNA or AA sequences.

### Usage

    where(x, pattern)

### Arguments

`x` | an object inheriting the class either `"DNAbin"` or `"AAbin"`.
`pattern` | a character string to be searched in `x`.

### Details

If `x` is a vector, the function returns a single vector giving the position(s) where the pattern was found. If `x` is a matrix or a list, it returns a list with the positions of the pattern for each sequence.

Patterns may be overlapping. For instance, if `pattern = "tata"` and the sequence starts with ‘tatata’, then the output will be c(1, 3).

### Value

a vector of integers or a list of such vectors.

### Author(s)

Emmanuel Paradis

### See Also

`DNAbin`, `image.DNAbin`, `AAbin`

### Examples

    data(woodmouse)
    where(woodmouse, "tata")
    ## with AA sequences:
    x <- trans(woodmouse, 2)
    where(x, "irk")

[Package ape version 5.6 Index]