closedGenomes

[ancetre.git] / art.tex

diff --git a/art.tex b/art.tex
index f3afb1821a3b6a5a6a4ac4077e8c9e82e7f16ad2..92a8c4838e950619c0280a5e8d64540401fdcbcc 100644 (file)
--- a/art.tex
+++ b/art.tex
@@ -13,15 +13,28 @@ To achieve this, the authors
   SNPs data.
 \end{enumerate}
 
   SNPs data.
 \end{enumerate}
 

-In~\cite{10.1371/journal.pone.0052841} the authors analyse 435 Mycobacterium Tuberculosis complex isolates of the same clade. By focusing on the H37Rv genome, 
+In~\cite{10.1371/journal.pone.0052841} the authors analyze 435 Mycobacterium Tuberculosis complex isolates of the same clade. By focusing on the H37Rv genome, 

 they produce 13382 SNPs. Later, they  compare  44 genomes to this one 
 they produce 13382 SNPs. Later, they  compare  44 genomes to this one 

-regarding these SNP. The way they extract this phylogenetical tree is 
+regarding these SNP. The way they extract this phylogenetic tree is 

 not detailed. They focus then on Percy256 and Percy556 since both these 
 genomes have a very long branch split from the  M. Canetti. They deduce then 
 a new lineage.
 
 
 
 not detailed. They focus then on Percy256 and Percy556 since both these 
 genomes have a very long branch split from the  M. Canetti. They deduce then 
 a new lineage.
 
 
 

+In~\cite{17623808}, the aim of the authors is to reconstruct
+the genome of the last common ancestor between Mycobacterium leprae
+(Ml) and Mycobacterium tuberculosis and (Mt).
+\JFC{On devrait appliquer notre approche et comparer les résultats.}
+The set of genes of genomes of these two complex 
+is enlarged with pseudo-genes which have been exhibit thanks 
+to a similarity analysis. They focus on the subset of ortholog genes 
+(how they extract them?).
+Thanks to the parsimony criterion
+(a (pseudo)gene is ancestral iff it is present in at least two of  mycobacterial lineages), the authors compute the set of genes, which are included in the ancestral genome.
+They apply again the parsimony criterion to establish the order of these genes in the ancestor’s chromosome.
+
+

 \paragraph{eukaryote}
 In~\cite{CGOT10}, the authors show how to reconstruct an ancestral genome of seven eukaryotes species (Saccharomyces cerevisiae, Candida glabrata, Zygosaccharomyces rouxii, Kluyveromyces lactis, Ashbya gossypii, Kluyveromyces thermotolerans, Saccharomyces kluyveri).
 Their method is as follows:
 \paragraph{eukaryote}
 In~\cite{CGOT10}, the authors show how to reconstruct an ancestral genome of seven eukaryotes species (Saccharomyces cerevisiae, Candida glabrata, Zygosaccharomyces rouxii, Kluyveromyces lactis, Ashbya gossypii, Kluyveromyces thermotolerans, Saccharomyces kluyveri).
 Their method is as follows:


@@ -29,7 +42,7 @@ Their method is as follows:
 \item the starting point is a set of markers covering a large
   part of the extant genomes and which are believed to
   be present in a unique exemplar in the ancestral genome.
 \item the starting point is a set of markers covering a large
   part of the extant genomes and which are believed to
   be present in a unique exemplar in the ancestral genome.

-\item first method: rearrangement methods and particularely median method. Authors even provide informations about medians in case of duplicated genomes or not.   
+\item first method: rearrangement methods and particularly median method. Authors even provide information about medians in case of duplicated genomes or not.   

 \item second method: physical mapping techniques by trying to guess
   which genes should be close to each other, 
   and propose a mapping that maximize an objective function.
 \item second method: physical mapping techniques by trying to guess
   which genes should be close to each other, 
   and propose a mapping that maximize an objective function.