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.
-
+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}
