From 141867311cf1b9e16801bf1cab297fb2f0621bc6 Mon Sep 17 00:00:00 2001
From: cguyeux <cguyeux@iut-bm.univ-fcomte.fr>
Date: Tue, 26 Mar 2013 10:27:11 +0100
Subject: [PATCH 1/1] Modifs

---
 main.tex         |  6 +++---
 presentation.tex | 25 ++++++++++++++++++++++---
 2 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/main.tex b/main.tex
index 4a7c86b..483e683 100755
--- a/main.tex
+++ b/main.tex
@@ -49,7 +49,7 @@
 \input{art}
 
 \section{Presentation of the Proposed Approach}\label{sec:ourapproach}
-
+\input{presentation}
 
 \section{Experiments}\label{sec:experiments}
 
@@ -62,8 +62,8 @@
 \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}
diff --git a/presentation.tex b/presentation.tex
index 2b31802..00c1138 100644
--- a/presentation.tex
+++ b/presentation.tex
@@ -1,5 +1,24 @@
 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}
-- 
2.39.5