\HeaderA{needwunsQS}{quadratic-space, simple gap implementation of Needleman-Wunsch
global alignment algorithm}{needwunsQS}
\aliasA{alignScore}{needwunsQS}{alignScore}
\methaliasA{alignScore.needwunsQS}{needwunsQS}{alignScore.needwunsQS}
\aliasA{needwunsQS,BString,character-method}{needwunsQS}{needwunsQS,BString,character.Rdash.method}
\aliasA{needwunsQS,character,BString-method}{needwunsQS}{needwunsQS,character,BString.Rdash.method}
\aliasA{needwunsQS,character,character-method}{needwunsQS}{needwunsQS,character,character.Rdash.method}
\aliasA{print.needwunsQS}{needwunsQS}{print.needwunsQS}
\keyword{models}{needwunsQS}
\begin{Description}\relax
quadratic-space, simple gap implementation of Needleman-Wunsch
global alignment algorithm
\end{Description}
\begin{Usage}
\begin{verbatim}
needwunsQS(s1, s2, substmat, gappen=8)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{s1}] s1: first string, an R character vector of length 1
or a \LinkA{BString}{BString} instance
\item[\code{s2}] s2: second string, same data type as \code{s1}
\item[\code{substmat}] substmat: matrix of alignment score values
\item[\code{gappen}] gappen: penalty for introducing a gap in the alignment
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
follows specification of Durbin, Eddy, Krogh, Mitchison (1998).
\end{Details}
\begin{Value}
an instance of the S3 class ``needwunsQS'', for which there are
print and alignScore methods.
\end{Value}
\begin{Author}\relax
Vince Carey <stvjc@channing.harvard.edu>
\end{Author}
\begin{References}\relax
R. Durbin, S. Eddy, A. Krogh, G. Mitchison, 
Biological Sequence Analysis, Cambridge UP 1998, sec 2.3.
\end{References}
\begin{Examples}
\begin{ExampleCode}
data(blosum50)
needwunsQS( "PAWHEAE", "HEAGAWGHEE", blosum50 )
\end{ExampleCode}
\end{Examples}