+\begin{frame}{Previous Contenders}
+ \begin{itemize}
+ \item Blastx
+ \item Rapsearch
+ \item mBlast
+ \item many, many, more
+ \end{itemize}
+\end{frame}
+
+
+\section{Diamond Advances}
+\begin{frame}{Diamond Methodology Advances}
+ \begin{itemize}
+ \item Seed and Extend
+ \item Reduced Alphabet
+ \item Spaced Seeds with Specific Seed Shape
+ \item Double Indexing
+ \end{itemize}
+\end{frame}
+
+\begin{frame}{Seed and Extend}
+ \begin{itemize}
+ \item Calculate an index
+ \item Look up matching indices in the database
+ \item Local string alignment using Smith-Waterman
+ \item Looks like blast, right?
+ \end{itemize}
+\end{frame}
+
+\begin{frame}{Reduced Alphabet}
+
+ \begin{itemize}
+ \item \colorbox{red}{LVI} \colorbox{red!10!white}{M} \colorbox{yellow}{C} \colorbox{black!50!white}{G} \colorbox{red!50!blue}{\textcolor{white}{STA}}
+ \colorbox{green}{P} \colorbox{red!50!blue!50!white}{F} \colorbox{red!50!blue!20!white}{Y} \colorbox{black}{\textcolor{white}{W}} \colorbox{blue}{\textcolor{white}{KREDNQ}}
+%- [KREDQN] [C] [G] [H] [ILV] [M] [F] [Y] [W] [P] [STA].
+ \item Smaller index sizes --- less memory usage
+ \item Greater sensitivity --- seed more likely to match
+ \item More likelihood of useless extensions --- only the seed matched
+ \end{itemize}
+ {\centering
+ \includegraphics[height=0.5\textheight,width=0.8\textwidth,keepaspectratio]{figures/reduced_alphabet.png}
+
+ \cite{Murphy.ea2000:Simplifiedaminoacidalphabets}
+ }
+
+\end{frame}
+
+\begin{frame}{Spaced Seeds with Specific Seed Shape}
+ \begin{itemize}
+ \item Spaced seeds are longer seeds in which only a subset of the
+ positions are used
+ \item For example, if
+ \begin{itemize}
+ \item the sequence was ABCDEFGHI
+ \item the seed shape was
+ 11100010
+ \item then you would query into the index with ABCG
+ \end{itemize}
+ \item Originally presented in PatternHunter\cite{Ma.ea2002:PatternHunterfasterandmore}
+ \item Why is this better than consecutive seeds?
+\end{itemize}
+\end{frame}
+
+\begin{frame}{Consecutive Seeds vs Spaced Seeds}
+ \begin{itemize}
+ \item Target Sequence: ABCDEFGHIJK
+ \item Sequenced Sequence: ABC\textcolor{red}{Z}EF\textcolor{red}{Y}HI\textcolor{red}{X}K
+ \item Seed Shape: 11100010 (4) and Consecutive: 1111 (4)
+ \end{itemize}
+% ABCZEFGHIYK
+% ABCDEFGHIJK
+% 11000010---
+% -11000010--
+% --11000010-
+% ---11000010
+
+ \begin{columns}
+ \column{0.6\textwidth}
+\begin{block}{Pathological example}
+ \begin{tabular}{c c c}
+ Shift & Spaced & Consecutive \\
+ 0 & ABCF=ABCF & ABCD≠ABCZ \\
+ 1 & BCDG≠BCZY & BCDE≠BCZE \\
+ 2 & CDEH≠CZEH & CDEF≠CZEF \\
+ 3 & DEFI≠ZEFI & DEFG≠ZEFY \\
+ 4 & EFGJ≠EFYW & EFGH≠EFYH \\
+ 5 & FGHK≠FYHK & FGHI≠FYHI \\
+ 6 & & GHIJ≠YHIW \\
+ 7 & & HIJK≠HIWK \\
+ \end{tabular}
+\end{block}
+ \column{0.4\textwidth}
+ \begin{itemize}
+ \item Spaced seed matches once
+ \item Consecutive seed never matches
+ \item Consecutive seed does more comparisons and may match
+ repeatedly
+ \end{itemize}
+\end{columns}
+\end{frame}