Modifs

diff --git a/main.tex b/main.tex
index 4a7c86bf526c2fd788a6af051d56b4d490947bee..483e683af152565628b5ca939d5dcfb2244c4214 100755 (executable)
--- a/main.tex
+++ b/main.tex
@@ -49,7 +49,7 @@
 \input{art}
 
 \section{Presentation of the Proposed Approach}\label{sec:ourapproach}
 \input{art}
 
 \section{Presentation of the Proposed Approach}\label{sec:ourapproach}

-
+\input{presentation}

 
 \section{Experiments}\label{sec:experiments}
 
 
 \section{Experiments}\label{sec:experiments}
 


@@ -62,8 +62,8 @@
 \input{closedgenomes}
 
 
 \input{closedgenomes}
 
 

-\section{Third Stage: Reconstruction of Ancestral Synteny Blocs for the two Closest Genomes}
-
+\section{Third Stage: Reconstruction of Ancestral Syntheny Blocks for the two Closest Genomes}
+\input{syntheny}

 \section{Fourth Stage: Filling holes in the Obtained Ancestral Genome}
 
 \section{Last Stage: to Reproduce the Process until Obtaining the Last Common Ancestor of the given set of Genomes}
 \section{Fourth Stage: Filling holes in the Obtained Ancestral Genome}
 
 \section{Last Stage: to Reproduce the Process until Obtaining the Last Common Ancestor of the given set of Genomes}

diff --git a/presentation.tex b/presentation.tex
index 2b31802b030129cc090e90761006a270a22ad7e5..00c11385d432c41730d30c0db51a7d2cd0226e0c 100644 (file)
--- a/presentation.tex
+++ b/presentation.tex
@@ -1,5 +1,24 @@
 Given a bacteria, various complete genomes can be found on the Internet.
 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
 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}