update memory usage

[chloroplast13.git] / annotated.tex

diff --git a/annotated.tex b/annotated.tex
index 46619ab9a42a64153ccd0cd2133a800e3363d40c..9ae72781d37552fa9a3c5357f690c290ffe9d31b 100644 (file)
--- a/annotated.tex
+++ b/annotated.tex
@@ -287,11 +287,11 @@ core genes with its two genomes parents.
 \subsection{Features visualization}
 
 The goal is to visualize results  by building a tree of evolution. All
 \subsection{Features visualization}
 
 The goal is to visualize results  by building a tree of evolution. All

-core  genes generated  represent  important information  in the  tree,
-because they  provide information about  the ancestors of two  or more
+core  genes generated  represent  an important information  in the  tree,
+because they  provide ancestor information of two  or more

 genomes. Each  node in the  tree represents one chloroplast  genome or
 genomes. Each  node in the  tree represents one chloroplast  genome or

-one predicted core called \textit{(Genes count:Family name\_Scientific
-names\_Accession number)}, while an edge is labeled with the number of
+one predicted core and labelled as \textit{(Genes count:Family name\_Scientific
+names\_Accession number)}. While an edge is labelled with the number of

 lost  genes from  a leaf  genome or  an intermediate  core  gene. Such
 numbers are  very interesting because  they give an  information about
 the evolution:  how many genes  were lost between two  species whether
 lost  genes from  a leaf  genome or  an intermediate  core  gene. Such
 numbers are  very interesting because  they give an  information about
 the evolution:  how many genes  were lost between two  species whether


@@ -315,6 +315,7 @@ The procedure used to built a phylogenetic tree is as follows:
 \item For each gene in a core gene, extract its sequence and store it in the database.
 \item Use multiple alignment tools such as (****to be write after see christophe****) 
 to align these sequences with each others.
 \item For each gene in a core gene, extract its sequence and store it in the database.
 \item Use multiple alignment tools such as (****to be write after see christophe****) 
 to align these sequences with each others.

+\item we use an outer-group genome from cyanobacteria to calculate distances.

 \item Submit the resulting aligned sequences to RAxML program to compute the distances and finally draw the phylogenetic tree.
 \end{enumerate} 
 
 \item Submit the resulting aligned sequences to RAxML program to compute the distances and finally draw the phylogenetic tree.
 \end{enumerate} 
 


@@ -324,7 +325,7 @@ to align these sequences with each others.
 \end{figure}
 
 \section{Implementation}
 \end{figure}
 
 \section{Implementation}

-We implemented four algorithms to extract maximum core genes from large amount of chloroplast genomes. Two algorithms used to extract core genes based on NCBI annotation, and the others based on dogma annotation tool. Evolutionary tree generated as a result from each method implementation. In this section, we will present the four methods, and how they can extract maximum core genes?, and how the developed code will generate the evolutionary tree.
+We implemented three algorithms to extract maximum core genes from large amount of chloroplast genomes. one algorithm used to extract core genes based on NCBI annotation, and the others based on NCBI and DOGMA annotation tool. Evolutionary tree generated as a result from each method implementation. In this section, we will present the three methods, and how they can extract maximum core genes?, and how the developed code will generate the evolutionary tree.

 
 \subsection{Extract Core Genes based on Gene Contents}
 
 
 \subsection{Extract Core Genes based on Gene Contents}
 


@@ -340,6 +341,11 @@ The pipeline of extracting core genes can summarize in the following steps accor
 \item Evolutionary tree will take place by using all data generated from step 1 and 4. The tree will also display the amount of genes lost from each intersection iteration. A specific excel file will be generated that store all the data in local database.
 \end{enumerate}
 
 \item Evolutionary tree will take place by using all data generated from step 1 and 4. The tree will also display the amount of genes lost from each intersection iteration. A specific excel file will be generated that store all the data in local database.
 \end{enumerate}
 

+\begin{figure}[H]
+  \centering \includegraphics[width=0.75\textwidth]{NCBI_mem}
+  \caption{Memory consuming from NCBI annotation}\label{Nmem}
+\end{figure}
+

 There main drawback with this method is genes orthography (e.g two different genes sequences with same gene name). In this case, Gene lost is considered by solving gene duplication based on first method to solve gene duplication.
 
 \subsubsection{Core Genes based on Dogma Annotation}  
 There main drawback with this method is genes orthography (e.g two different genes sequences with same gene name). In this case, Gene lost is considered by solving gene duplication based on first method to solve gene duplication.
 
 \subsubsection{Core Genes based on Dogma Annotation}  


@@ -354,6 +360,11 @@ extracting core genes based on genes names and counts summarized in the followin
 
 \end{enumerate}
 
 
 \end{enumerate}
 

+\begin{figure}[H]
+  \centering \includegraphics[width=0.75\textwidth]{dogma_mem}
+  \caption{Memory consuming from DOGMA annotation}\label{dmem}
+\end{figure}
+

 
 The main drawback from the method of extracting core genes based on gene names and counts 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.               
 
 
 The main drawback from the method of extracting core genes based on gene names and counts 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.