From: bassam al-kindy <bassam.al-kindy@lifc>
Date: Tue, 22 Oct 2013 10:46:40 +0000 (+0200)
Subject: update step III from the algorithm.
X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/chloroplast13.git/commitdiff_plain/9fa4c949043a414e7632a542fe99e429060e6bf0

update step III from the algorithm.
---

diff --git a/annotated.tex b/annotated.tex
index 86259a0..c2d70c9 100644
--- a/annotated.tex
+++ b/annotated.tex
@@ -74,11 +74,12 @@ The Algorithm of construction the matrix and extracting maximum core genes where
 \end{algorithmic}
 \end{algorithm}
 
-In this algorithm, \textit{GenomeList} represents the database.
+In this algorithm, \textit{GenomeList} represents the database.\\
 
-\textbf{Step III: Draw the Tree}\\
+\textbf{Step III: Drawing the Tree}\\
+The main objective here is to the results for visualizing a tree of evolution. We use here a directed graph from Dot graph package\cite{gansner2002drawing} from Graphviz library. The system produce this tree automatically by using all information available in a database. Core genes generated with their genes can be very important information, because they represent also the ancestor information for two genomes. In this tree, each node represent genome or core genes as \textit{(Genes count:Family name,Scientific name,Accession number)}, Edges here represent the number of lost genes from genomes-core or core-core intersection. The number of lost genes here can be an important factor for evolution, it represents how much lost of genes for the species in same or different families. By the principle of classification, small genes lost among species can say that these species are closely together and belongs to same family, while big genes lost means that species is far to be in the same family. To see the picture clearly, Phylogenetic tree is an evolutionary tree generated also by the system. Generating this tree is based on the distances among genes sequences. There are many resources to build such tree (for example: PHYML\cite{guindon2005phyml}, RAxML{\cite{stamatakis2008raxml}\cite{stamatakis2005raxml}, BioNJ , and TNT\cite{goloboff2008tnt}}. We consider to use RAxML\cite{stamatakis2008raxml}\cite{stamatakis2005raxml} to generate this tree.   
 
-The main drawback from this method is that we can not depending only on genes names because of three causes: first, the genome may have not totally named, so we will have some lost sequences. Second, may we have two genes sharing the same name, while their sequences are different. Third, we need to annotate 99 genomes.
+The main drawback from this method is that we can not depending only on genes names because of three causes: first, the genome may have not totally named (This can be found in early versions of NCBI genomes), so we will have some lost sequences. Second, we may have two genes sharing the same name, while their sequences are different. Third, we need to annotate all the genomes.
 
 \subsubsection{Extracting Core genome from NCBI gene contents}
 
diff --git a/biblio.bib b/biblio.bib
index 2225ccf..92db33a 100644
--- a/biblio.bib
+++ b/biblio.bib
@@ -68,6 +68,14 @@ author={Tannier, Eric},
 pages={1-12}
 }
 
+@article{gansner2002drawing,
+  title={Drawing graphs with dot},
+  author={Gansner, Emden and Koutsofios, Eleftherios and North, Stephen},
+  journal={Retrieved June},
+  volume={13},
+  pages={2005},
+  year={2002}
+}
 
 @article{10.1371/journal.pone.0052841,
     author = {Blouin, Yann AND Hauck, Yolande AND Soler, Charles AND Fabre, Michel AND Vong, Rithy AND Dehan, Céline AND Cazajous, Géraldine AND Massoure, Pierre-Laurent AND Kraemer, Philippe AND Jenkins, Akinbowale AND Garnotel, Eric AND Pourcel, Christine AND Vergnaud, Gilles},
@@ -122,6 +130,46 @@ NUMBER = {172004},
 PAGES = {3252-3255},
 URL={http://www.biosci.utexas.edu/ib/faculty/jansen/pubs/Wyman%20et%20al.%202004.pdf},
 }
+@article{guindon2005phyml,
+  title={PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference},
+  author={Guindon, Stephane and Lethiec, Franck and Duroux, Patrice and Gascuel, Olivier},
+  journal={Nucleic acids research},
+  volume={33},
+  number={suppl 2},
+  pages={W557--W559},
+  year={2005},
+  publisher={Oxford Univ Press}
+}
+
+@article{goloboff2008tnt,
+  title={TNT, a free program for phylogenetic analysis},
+  author={Goloboff, Pablo A and Farris, James S and Nixon, Kevin C},
+  journal={Cladistics},
+  volume={24},
+  number={5},
+  pages={774--786},
+  year={2008},
+  publisher={Wiley Online Library}
+}
+
+@article{stamatakis2008raxml,
+  title={The RAxML 7.0. 4 Manual},
+  author={Stamatakis, Alexandros},
+  journal={Department of Computer Science. Ludwig-Maximilians-Universit{\"a}t M{\"u}nchen},
+  year={2008}
+}
+@article{stamatakis2005raxml,
+  title={RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees},
+  author={Stamatakis, Alexandros and Ludwig, Thomas and Meier, Harald},
+  journal={Bioinformatics},
+  volume={21},
+  number={4},
+  pages={456--463},
+  year={2005},
+  publisher={Oxford Univ Press}
+}
+
+
 @article{Bakke2009,
     author = {Bakke, Peter AND Carney, Nick AND DeLoache, Will AND Gearing, Mary AND Ingvorsen, Kjeld AND Lotz, Matt AND McNair, Jay AND Penumetcha, Pallavi AND Simpson, Samantha AND Voss, Laura AND Win, Max AND Heyer, Laurie J. AND Campbell, A. Malcolm},
     journal = {PLoS ONE},