Given a bacteria, various complete genomes can be found on the Internet.
For each genome, the complete records in fasta file are downloaded from the
NCBI nucleotide website. Then, GenemarkS is queried to find open reading
frames we will improperly called genes in the remainder of this document.
Another approach could be to download directly the coding sequence files from
the NCBI, however our experiments show that the annotated files are sometimes
really problematic. Furthermore, almost thirty gene prediction software (GPS) exist,
and they potentially can be used with various parameters, leading to numerous
different annotated genomes. For our part, we have chosen the three most famous
GPS, namely Glimmer, GeneMark, and Rast (see Table~\ref{GPS}).
\begin{table}
\centering
\begin{tabular}{|l|c|}
\hline
Gene prediction software & Good ORFs \\
\hline
Glimmer & 2558 \\
Genemask & 2768 \\
Rast & 2560 \\
\hline
\end{tabular}
\caption{Gene prediction scores of the best GPS on H37Rv}
\label{GPS}
\end{table}
