From: Michel Salomon <salomon@caseb.iut-bm.univ-fcomte.fr>
Date: Mon, 2 Dec 2013 13:04:01 +0000 (+0100)
Subject: Merge branch 'master' of ssh://bilbo/chloroplast13
X-Git-Url: https://bilbo.iut-bm.univ-fcomte.fr/and/gitweb/chloroplast13.git/commitdiff_plain/38c1dcfbefcbed8161d2e34081f977f7e1222f64?hp=-c

Merge branch 'master' of ssh://bilbo/chloroplast13
---

38c1dcfbefcbed8161d2e34081f977f7e1222f64
diff --combined annotated.tex
index e9e3049,3a97542..819cc33
--- a/annotated.tex
+++ b/annotated.tex
@@@ -47,11 -47,11 +47,11 @@@ that stores annotated and/or unannotate
  considered the GenBank-NCBI \cite{Sayers01012011} database as sequence
  database:  99~genomes of chloroplasts  were retrieved.   These genomes
  lie in  the eleven type  of chloroplast families and  Table \ref{Tab2}
- summarizes their distribution in our dataset.
+ summarizes their distribution in our dataset.\\
  
  \begin{figure}[h]  
    \centering
-     \includegraphics[width=0.75\textwidth]{generalView}
+     \includegraphics[width=0.8\textwidth]{generalView}
  \caption{A general overview of the annotation-based approach}\label{Fig1}
  \end{figure}
  
@@@ -240,25 -240,36 +240,25 @@@ score_{ij}=\vert g_i \cap g_j\ver
  \label{Eq1}
  \end{equation}
  \noindent where $1 \leq i \leq n$, $1 \leq j \leq n$, and $g_i, g_j$ are 
 -genomes. The  generation of a new  core gene depends obviously on the
 -value of intersection scores $score_{ij}$:
 +genomes. The  generation of a new  core gene depends  obviously on the
 +value  of the  intersection scores  $score_{ij}$. More  precisely, the
 +idea is  to consider a  pair of genomes  such that their score  is the
 +largest element in ICM. These two genomes are then removed from matrix
 +and the  resulting new  core genome is  added for the  next iteration.
 +The ICM is then updated to take into account the new core gene: new IS
 +values are computed for it. This process is repeated until no new core
 +gene can be obtained.
  
 -% TO BE CONTINUED
 -
 -$$
 -\text{new Core} = 
 -\begin{cases}
 -\text{Ignored} & \text{if $\textit{score}=0$;} \\
 -\text{new Core id} & \text{if $\textit{Score}>0$.}
 -\end{cases}
 -$$
 -
 -if     $\textit{Score}=0$     then     we    have     \textit{disjoint
 -relation} \emph{i.e.},  no common genes between two  genomes.  In this
 -case  the  system  ignores  the   genome  that  annul  the  core  gene
 -size. Otherwise, The system removes these two genomes from ICM and add
 -new  core  genome  with a  \textit{coreID}  of  them  to ICM  for  the
 -calculation in  next iteration. This  process reduces the size  of ICM
 -and repeats until all genomes  are treated \emph{i.e.} ICM has no more
 -genomes.  We observe  that ICM is very large because  of the amount of
 -data that it stores. This results  to be time and memory consuming for
 -calculating  the  intersection  scores.   To  increase  the  speed  of
 -calculations, it  is sufficient to  only calculate the  upper triangle
 -scores. The time complexity for this process after enhancement is thus
 -$O(\frac{n.(n-1)}{2})$.   Algorithm   \ref{Alg1:ICM}  illustrates  the
 -construction of  the ICM matrix and  the extraction of  the core genes
 -where \textit{GenomeList},  represents the database  where all genomes
 -data are stored. At each iteration, it computes the maximum core genes
 -with its two genomes parents.
 +We  can observe  that  the ICM  is very  large  due to  the amount  of
 +data. As a consequence, the  computation of the intersection scores is
 +both  time and  memory consuming.  However,  since ICM  is a  symetric
 +matrix we can reduce the  computation overhead by considering only its
 +triangular  upper part.  The  time complexity  for this  process after
 +enhancement is thus $O(\frac{n.(n-1)}{2})$.  Algorithm ~\ref{Alg1:ICM}
 +illustrates the construction  of the ICM matrix and  the extraction of
 +the  core  genes, where  \textit{GenomeList}  represents the  database
 +storing all genomes  data. At each iteration, it  computes the maximum
 +core genes with its two genomes parents.
  
  % ALGORITHM HAS BEEN REWRITTEN
  
@@@ -321,7 -332,7 +321,7 @@@ to align these sequences with each othe
  \end{enumerate} 
  
  \begin{figure}[H]
-   \centering \includegraphics[width=0.75\textwidth]{Whole_system}
+   \centering \includegraphics[width=0.8\textwidth]{Whole_system}
    \caption{Overview of the pipeline}\label{wholesystem}
  \end{figure}