\HeaderA{matchingSites}{Report IUPAC consensus occurrences in a fasta file}{matchingSites}
\keyword{methods}{matchingSites}
\begin{Description}\relax
This function reports all occurrences of a consensus sequence in a fasta
file. It can be used to extract transcription factor binding sites
predicted by BCRANK or other motif search methods.
\end{Description}
\begin{Usage}
\begin{verbatim}
matchingSites(fafile, motifSequence, revComp=TRUE, strip.desc=TRUE)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{fafile}] a ranked fasta file containing DNA sequences.
\item[\code{motifSequence}] a character vector in IUPAC coding representing a
DNA sequence.
\item[\code{revComp}] set to TRUE if the reverse complement also be matched.
\item[\code{strip.desc}] An argument used by the function \code{HYPERLINK(readFASTA())(readFASTA())}.
It specifies whether or not the ">" marking at the beginning of description lines should be removed.
\end{ldescription}
\end{Arguments}
\begin{Value}
Returns a data frame with positions, strand and DNA sequence for the
matching sites.
\end{Value}
\begin{Author}\relax
Adam Ameur, \email{adam.ameur@lcb.uu.se}
\end{Author}
\begin{References}\relax
Ameur, A., Rada-Iglesias, A., Komorowski, J., Wadelius, C. Novel
algorithm and ChIP-analysis identifies candidate functional SNPs. Submitted
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{bcrank}{bcrank}}
\end{SeeAlso}

