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%\VignetteIndexEntry{upstream sequence management for yeast}
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\title{The sceUpstr support in package harbChIP}
\author{HJB/VJC}
\maketitle

\tableofcontents

\section{Introduction}

The intent of this package is to allow code like the following:
\begin{Schunk}
\begin{Sinput}
> library(harbChIP)
> data(sceUpstr)
> sceUpstr
\end{Sinput}
\begin{Soutput}
upstreamSeqs instance, organism  sce 
There are  6674  entries
first keys: 
[1] "YAL001C" "YAL002W" "YAL003W" "YAL004W" "YAL005C"
\end{Soutput}
\begin{Sinput}
> getUpstream("YAL001C", sceUpstr)
\end{Sinput}
\begin{Soutput}
$YAL001C
  500-letter "DNAString" instance
Value: CTGTACCACTATAATAATTTATCTTGATCGTATTA...GACGTTTGGTTGAAGCCAACTAGCCACAAGAAAA
\end{Soutput}
\end{Schunk}

\section{Building the sceUpstr object}

Upstream sequences of length 500bp were obtained from the SGD website:\\
\texttt{www.yeastgenome.org -> Download Data -> FTP}\\
\texttt{sequence/genomic\_sequence/orf\_dna/archive/utr5\_sc\_500.20040206.fasta.gz}

\begin{Schunk}
\begin{Sinput}
> fname = system.file("extdata/utr5_sc_500_20040206.fasta", package = "sceUpstr")
> utr5 = readFASTA(fname)
> sceUpstr = buildUpstreamSeqs2(utr5)
> save(sceUpstr, file = "sceUpstr.rda")
\end{Sinput}
\end{Schunk}

\section{Checking a finding of Harbison et al.}

It is asserted in Fig 1 B of the paper that GGCGCTA is specifically bound by Snt2.
We will examine the frequency of this heptamer in upstream regions and relate to the
binding ratio distribution.

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