From: Jean-François Couchot <couchot@bilbo.iut-bm.univ-fcomte.fr>
Date: Thu, 21 Mar 2013 07:25:46 +0000 (+0100)
Subject: t
X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/ancetre.git/commitdiff_plain/ebcab8d2a6e4951ed9a20959ae92787dc5d3af65?hp=-c

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+The approache is further based on the ability to decide how far is each 
+genome from each others. To achieve this, we combine XXX metrics which are 
+detailed in this part.
+
+\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 
+$\dot{x}= \{y  | x \sim y\}$. 
+
+\JFC{Il faudrait être cohérent: deux génomes proches devraient partout avoir 
+soit une métrique élevée soit une métrique très faible}
+
+%1/ On SNPs of the core genome strict
+All the $y$ are thus aligned 
+thanks to a global alignment tool. The SNPs may thus be extracted.
+For each genome, one can thus compute the vector of boolean values 
+memorizing at index $i$ wether the SNP $i$ is present in one of its gene 
+(postive value) or  not (null value). 
+A Hamming distance between two vectors allows to build the distance 
+between two genes. 
+This metric is further refered as to $m_S$.
+
+% plus il y a de diff, plus le nombre est élevé
+
+
+%2/ On SNPs of the core genome strict, each gene having the same weight
+The $m_S$ method does not consider genes to have the same incidence in the 
+metric value. A gene with many SNPs has a larger influence in 
+the metric computation than a gene with fewer ones. 
+The metric further refered as to $m_{|S|}$ gives the same weight to each gene
+without considering the number of SNP it contains. 
+
+% plus il y a de diff, plus le nombre est élevé
+
+
+%3/ On gene content (symmetric difference)
+The third metric consider the symetric difference $\Delta$ 
+between the two sets $G_1$ and $G_2$ of genes.
+$$
+G_1\Delta G2 = 
+(G1\cup G_2)\setminus (G1\cap G_2) = (G1\setminus G_2)\cup(G_2\setminus G1) 
+$$
+\end{document}
+
+% 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.