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\name{where}
\alias{where}
\title{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{
\item{x}{an object inheriting the class either \code{"DNAbin"} or
\code{"AAbin"}.}
\item{pattern}{a character string to be searched in \code{x}.}
}
\details{
If \code{x} is a vector, the function returns a single vector giving
the position(s) where the pattern was found. If \code{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 \code{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{Emmanuel Paradis}
\seealso{
\code{\link{DNAbin}}, \code{\link{image.DNAbin}}, \code{\link{AAbin}}
}
\examples{
data(woodmouse)
where(woodmouse, "tata")
## with AA sequences:
x <- trans(woodmouse, 2)
where(x, "irk")
}
\keyword{manip}
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