From: Jean-François Couchot <couchot@couchot.iut-bm.univ-fcomte.fr>
Date: Fri, 22 Mar 2013 13:54:40 +0000 (+0100)
Subject: methode yu lin esquissée
X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/ancetre.git/commitdiff_plain/816fb65d854cd25faf1502a4dacea06b10e27ad3?hp=-c

methode yu lin esquissée
---

816fb65d854cd25faf1502a4dacea06b10e27ad3
diff --combined closedgenomes.tex
index ed2ad82,bfe1c1b..5ee33c2
--- a/closedgenomes.tex
+++ b/closedgenomes.tex
@@@ -2,7 -2,7 +2,7 @@@ The approach is further based on the ab
  genome from each others. To achieve this, we combine XXX metrics which are 
  detailed in this part.
  
- \subsection{Core SNP based metric} 
+ \subsection{Core SNP based Metric} 
  Due to the definition of the core genome, for each element $\dot{x}$ 
  in this set, there is a gene $x \in \dot{x}$ in each genome. 
  Let us consider a class 
@@@ -33,7 -33,7 +33,7 @@@ without considering the number of SNP i
  
  % plus il y a de diff, plus le nombre est élevé
  
- \subsection{Symmetric Difference based metric}
+ \subsection{Symmetric Difference based Metric}
  The third metric consider the symmetric difference $\Delta$ 
  between the two sets $G_1$ and $G_2$ of genes recalled hereafter
  $$
@@@ -50,9 -50,23 +50,30 @@@ one
  This metric is equal to the Hamming distance between the two corresponding  
  vectors of Boolean values.
  
+ % plus il y a de diff, plus le nombre est élevé
+ 
+ 
 -\subsection{}
+ 
+ % 4/ Using EPFL method
 +\subsection{Adjacency based metric}
 +23424133
- % 4/ Using EPFL method
- % 5/ On size of the biggest syntheny bloc
- % 6/ On average size of syntheny blocs
- % 7/ On number of syntheny blocs.
++
++
++
++
++
++
+ \subsection{Shared Synteny based Metric}
+ Given two genomes abstracted as sequences of classes, it is classical
+ to computes all the maximum shared synteny chains. 
+ 
+ % Attention ici, moins il y a de diff, plus le nombre est élevé
+ There are then three issues with such a set of shared synteny chains:
+ \begin{itemize}
+ \item let $m_{Y}$ be the metric, which returns the 
+ length of the largest chains;
+ \item let $m_{\overline{Y}}$ be the metric, which returns the 
+ average length of synteny chains;
+ \item finally, let $m_{|Y|}$ be the metric, which returns the 
+ number of synteny chains.
+ \end{itemize}