\HeaderA{matchSeeds}{A function to match seed regions to sequences.}{matchSeeds}
\keyword{manip}{matchSeeds}
\begin{Description}\relax
Given an input set of seed regions and a set of sequences all locations
of the seed regions (exact matches) within the sequences are found.
\end{Description}
\begin{Usage}
\begin{verbatim}
matchSeeds(seeds, seqs)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{seeds}] The seeds, or short sequences, to match. 
\item[\code{seqs}] The sequences to find matches in. 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
We presume that the problem is an exact matching problem and that
all sequences are in the correct orientation for that.  If, for
example, you start with seed regions from a microRNA (for \code{seeds})
and 3'UTR sequences (for \code{seqs}), then you would want to reverse
complement one of the two sequences. And make sure all sequences
are either DNA or RNA.

Names from either \code{seeds} or \code{seqs} are propogated, as much
as is possible.
\end{Details}
\begin{Value}
A list containing one entry for each element of \code{seeds} that had
at least one match in one entry of \code{seqs}. Each element of this list
is a named vector containing the elements of \code{seqs} that the corresponding
seed has an exact match in.
\end{Value}
\begin{Author}\relax
R. Gentleman
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{seedRegions}{seedRegions}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(hsSeqs)
data(s3utr)
hSeedReg = seedRegions(hsSeqs)
comphSeed = as.character(reverseComplement(RNAStringSet(hSeedReg)))
comph = RNA2DNA(comphSeed)
mx = matchSeeds(comph, s3utr)
\end{ExampleCode}
\end{Examples}

