\HeaderA{phiX174Phage}{Versions of bacteriophage phiX174 complete genome and sample short reads}{phiX174Phage}
\aliasA{quPhiX174}{phiX174Phage}{quPhiX174}
\aliasA{srPhiX174}{phiX174Phage}{srPhiX174}
\aliasA{wtPhiX174}{phiX174Phage}{wtPhiX174}
\keyword{datasets}{phiX174Phage}
\begin{Description}\relax
Six versions of the complete genome for bacteriophage \eqn{\phi}{} X174 as well
as a small number of Solexa short reads, qualities associated with those short
reads, and counts for the number times those short reads occurred.
\end{Description}
\begin{Details}\relax
The \code{phiX174Phage} object is a \code{DNAStringSet} containing the
following six naturally occurring versions of the bacteriophage \eqn{\phi}{} X174
genome cited in Smith et al.:

\describe{
\item[Genbank:] The version of the genome from GenBank (NC\_001422.1, GI:9626372).
\item[RF70s:] A preparation of \eqn{\phi}{} X double-stranded replicative form (RF) of DNA
by Clyde A. Hutchison III from the late 1970s.
\item[SS78:] A preparation of \eqn{\phi}{} X virion single-stranded DNA from 1978.
\item[Bull:] The sequence of wild-type \eqn{\phi}{} X used by Bull et al.
\item[G'97:] The \eqn{\phi}{} X replicative form (RF) of DNA from Bull et al.
\item[NEB'03:] A \eqn{\phi}{} X replicative form (RF) of DNA from New England BioLabs (NEB).  
}

The \code{srPhiX174} object is a \code{DNAStringSet} containing short reads
from a Solexa machine.

The \code{quPhiX174} object is a \code{BStringSet} containing Solexa quality
scores associated with \code{srPhiX174}.

The \code{wtPhiX174} object is an integer vector containing counts associated
with \code{srPhiX174}.
\end{Details}
\begin{References}\relax
\url{http://www.genome.jp/dbget-bin/www_bget?refseq+NC_001422}

Bull, J. J., Badgett, M. R., Wichman, H. A., Huelsenbeck, Hillis, D. M., Gulati, A., Ho, C. \& Molineux, J.
(1997) Genetics 147, 1497-1507.

Smith, Hamilton O.; Clyde A. Hutchison, Cynthia Pfannkoch, J. Craig Venter (2003-12-23).
"Generating a synthetic genome by whole genome assembly: \{phi\}X174 bacteriophage from synthetic oligonucleotides".
Proceedings of the National Academy of Sciences 100 (26): 15440-15445. doi:10.1073/pnas.2237126100.
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(phiX174Phage)
nchar(phiX174Phage)
genBankPhage <- phiX174Phage[[1]]
genBankSubstring <- substring(genBankPhage, 2793-34, 2811+34)

data(srPhiX174)
srPhiX174
quPhiX174
summary(wtPhiX174)

alignPhiX174 <-
  pairwiseAlignment(srPhiX174, genBankSubstring,
                    patternQuality = SolexaQuality(quPhiX174),
                    subjectQuality = SolexaQuality(99L),
                    type = "global-local")
summary(alignPhiX174, weight = wtPhiX174)
\end{ExampleCode}
\end{Examples}

