diff --git a/docs/programmers/tutorials/workflows/part04.tex b/docs/programmers/tutorials/workflows/part04.tex index e9324491..d6b31c9b 100644 --- a/docs/programmers/tutorials/workflows/part04.tex +++ b/docs/programmers/tutorials/workflows/part04.tex @@ -418,8 +418,8 @@ \+ The command-line invocation for one such comparison would look like this: \begin{sh} -$ blastpgp -i new.faa -d known.faa \ - -e 1e-6 -m 9 -o output.txt +$ blastp -query new.faa -subject known.faa \ + -evalue 1e-6 -outfmt 9 \end{sh}%$ \end{frame} @@ -436,14 +436,15 @@ where: \begin{itemize} \item Option \texttt{-e} (alias: \texttt{-{}-e-value}) takes a floating point threshold argument $T$; - \item Option \texttt{-m} (alias: \texttt{--output-format}) takes a single-digit integer argument $F$; + \item Option \texttt{-m} (alias: \texttt{-{}-output-format}) takes a single-digit integer argument $F$; \item Arguments \texttt{new.faa}, \texttt{k1.faa}, etc. are files. \end{itemize} \+ The script should generate and run comparisons between \texttt{new.faa} and each of the {k$N$.faa}. Each 1-1 comparison should run as a separate task. All of them share the same - settings for the \texttt{-e} and \texttt{-m} options for \texttt{blastpgp}. + settings for the \texttt{-evalue} and \texttt{-outfmt} options for + \texttt{blastp}. \end{exercise*} \end{frame}