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part04: Fix BLAST invocation.
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Need to use BLAST+, Debian/Ubuntu package `ncbi-blast+`.
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riccardomurri committed Jul 13, 2016
1 parent 26dd3db commit aca2a58
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9 changes: 5 additions & 4 deletions docs/programmers/tutorials/workflows/part04.tex
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\+ 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}

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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}
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