\end{itemize}
\end{frame}
-\section{Usage}
-
-\begin{frame}{DIAMOND Usage}
- \begin{itemize}
- \item Make the diamond database:
- \texttt{diamond makedb --in foo.fasta --db foo.dmnd;}
- \item Run the diamond query:
- \texttt{diamond blastx --db foo.diamond --threads 24 --query bar.fasta --daa bar\_diamond.txt}
- \end{itemize}
-\end{frame}
-
\section{Comparison}
\subsection{Speed}
\begin{frame}{Speed of DIAMOND}
- \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_a.jpg}
+ \begin{center}
+ \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_a.jpg}
+ \end{center}
\end{frame}
\subsection{Accuracy}
\begin{frame}{Accuracy of DIAMOND: Any success}
- \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_b.jpg}
+ \begin{center}
+ \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_b.jpg}
+ \end{center}
\end{frame}
\begin{frame}{Accuracy of DIAMOND: Matches blastx}
- \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_c.jpg}
+ \begin{center}
+ \includegraphics[width=\textwidth,height=0.8\textheight,keepaspectratio]{diamond_paper_figures/diamond_F1_c.jpg}
+ \end{center}
\end{frame}
+\section{Usage}
+
+\begin{frame}{DIAMOND Usage}
+ \begin{itemize}
+ \item Make the diamond database:
+ \texttt{diamond makedb --in foo.fasta --db foo.dmnd;}
+ \item Run the diamond query:
+ \texttt{diamond blastx --db foo.diamond --threads 24 --query bar.fasta --daa bar\_diamond.txt}
+ \end{itemize}
+\end{frame}
+
+
+\subsection{Output}
+\begin{frame}{DIAMOND Output}
+ \begin{itemize}
+ \item Standard BLASTx output
+ \item Equivalent evalues and bit scores
+ \item An example from \textit{Spalax} (the top two proteins are
+ isoforms):
+ \end{itemize}
+ \tiny
+ \begin{tabular}{c c c c c c c c c c c c}
+ query & match & \% ident & length & \# mm & gap & qst & qstp & sstart & sstop & evalue & score \\
+c18\_g1\_i1 & ...065786 & 94.5 & 361 & 20 & 0 & 2 & 1084 & 992 & 1352 & 5.7e-203 & 704.9 \\
+c18\_g1\_i1 & ...081540 & 94.5 & 361 & 20 & 0 & 2 & 1084 & 940 & 1300 & 5.7e-203 & 704.9 \\
+c18\_g1\_i1 & ...142322 & 48.8 & 361 & 178 & 3 & 5 & 1078 & 944 & 1300 & 5.9e-99 & 359.4 \\
+c18\_g1\_i1 & ...039711 & 48.8 & 361 & 178 & 3 & 5 & 1078 & 936 & 1292 & 5.9e-99 & 359.4 \\
+c18\_g1\_i1 & ...141518 & 43.0 & 230 & 124 & 3 & 5 & 685 & 936 & 1161 & 1.7e-50 & 198.4 \\
+\end{tabular}
+\end{frame}
+
+
\section*{References}