Merge branch 'master' of ssh://bilbo.iut-bm.univ-fcomte.fr/chloroplast13

diff --git a/annotated.tex b/annotated.tex
index 2729939cf32eeb8174cb5ad82402619f3f3e31f3..81dcfc4bcd7ef2bbc6c18d4152d30bb8bb499f1f 100644 (file)
--- a/annotated.tex
+++ b/annotated.tex
@@ -11,7 +11,7 @@ In last stage, features visualization represents methods to visualize genomes an
 A Local database attached with each pipe stage is used to store all the informations of extraction process. The output from each stage in our system will be an input to the second stage and so on.
 
 \subsection{Genomes Samples}
-In this research, we retrieved genomes of Chloroplasts from NCBI. Ninety nine genome of them were considered to work with. These genomes lies in the eleven type of chloroplast families. The distribution of genomes is illustrated in detail in Table \ref{Tab2}.
+In this research, we retrieved genomes of Chloroplasts from NCBI. Ninety nine genome of them were considered to work with. These genomes lies in the eleven type of chloroplast families. The distribution of genomes is illustrated in detail in Table~\ref{Tab2}.
 
 \input{population_Table}       
 

diff --git a/main.tex b/main.tex
index 4d642f06bb23f1b57b37ab0aad34dffeb0d88668..162054bae25892c41960d305f5644b02dad8dc35 100755 (executable)
--- a/main.tex
+++ b/main.tex
@@ -7,7 +7,7 @@
 \usepackage{algorithm}
 \usepackage{algorithmic}
 \usepackage{pdflscape}
-\usepackage{longtable}
+\usepackage{multirow,longtable}
 \usepackage{amsmath,mathtools}
 \usepackage[utf8]{inputenc}
 

diff --git a/population_Table.tex b/population_Table.tex
index 974ea88c2e1772730cb768dddd899087abae3a07..9915d1a937f064cd401e4b0b1f16e40a5cec3a1f 100644 (file)
--- a/population_Table.tex
+++ b/population_Table.tex
@@ -1,121 +1,170 @@
-\footnotesize 
-\begin{tiny}
-\setlength\LTleft{50pt}            
-\setlength\LTright{0pt}       
 \begin{center}  
-\begin{longtable}{@{\extracolsep{2pt}}llll@{}}
-\caption[NCBI Genomes Families]{List of family groups of Chloroplast Genomes from NCBI\label{Tab2}}\\
-% Heading
-       \hline\hline
-       {\textbf{Family}}&{\textbf{Counts}} & {\textbf{Accession No}} & {\textbf{Scientific Name}} \\ 
-       \hline
+  
+  \begin{table}
+    \tiny
+    \begin{minipage}{0.50\textwidth}
+      \setlength{\tabcolsep}{4pt}
+      \begin{tabular}{|p{0.1cm}|p{0.1cm}|p{1.3cm}|p{3cm}|}
+      \hline
+      {{F.}}&{{\#}} & {{Acc. No}} & {{Scientific Name}} \\ 
+      \hline
        %Entering First line
-         & & NC\_001713.1 & Odontella sinensis \\ 
-         & & NC\_008588.1 & Phaeodactylum tricornutum \\ 
-         & & NC\_010772.1 & Heterosigma akashiwo \\ 
-         & & NC\_011600.1 & Vaucheria litorea \\ 
-         & & NC\_012903.1 & Aureoumbra lagunensis \\ 
-         Brown Algae & 11 & NC\_014808.1 & Thalassiosira oceanica \\ 
-         & & NC\_015403.1 & Fistulifera sp \\ 
-         & & NC\_016731.1 & Synedra acus \\ 
-         & & NC\_016735.1 & Fucus vesiculosus \\ 
-         & & NC\_018523.1 & Saccharina japonica \\ 
-         & & NC\_020014.1 & Nannochloropsis gadtina \\ [1ex]
-       %Entering second group
-         & & NC\_000925.1 & Porphyra purpurea \\ 
-         Red Algae & 3 & NC\_001840.1 & Cyanidium caldarium \\ 
-         & & NC\_006137.1 & Gracilaria tenuistipitata \\ [1ex]
-        %Entering third group
-         & & NC\_000927.1 & Nephroselmis olivacea \\ 
-         & & NC\_002186.1 & Mesotigma viride \\ 
-         & & NC\_005353.1 & Chlamydomonas reinhardtii \\ 
-         & & NC\_008097.1 & Chara vulgaris \\ 
-         & & NC\_008099.1 & Oltmannsiellopsis viridis \\ 
-         & & NC\_008114.1 & Pseudoclonium akinetum \\ 
-         & & NC\_008289.1 & Ostreococcus tauri \\ 
-         & & NC\_008372.1 & Stigeoclonium helveticum \\ 
-         Green Algae & 17 & NC\_008822.1 & Chlorokybus atmophyticus \\ 
-         & & NC\_011031.1 & Oedogonium cardiacum \\ 
-         & & NC\_012097.1 & Pycnococcus provaseolii \\ 
-         & & NC\_012099.1 & Pyramimonas parkeae \\ 
-         & & NC\_012568.1 & Micromonas pusilla \\ 
-         & & NC\_014346.1 & Floydiella terrestris \\ 
-         & & NC\_015645.1 & Schizomeris leibleinii \\ 
-         & & NC\_016732.1 & Dunaliella salina \\ 
-         & & NC\_016733.1 & Pedinomonas minor \\ [1ex] 
-        %Entering fourth group
-         & & NC\_001319.1 & Marchantia polymorpha \\ 
-         Brypoytes & 3 & NC\_004543.1 & Anthoceros formosae \\ 
-         & & NC\_005087.1 & Physcomitrella patens \\ [1ex]
-        %Entering fifth group
-         & & NC\_014267.1 & Kryptoperidinium foliaceum \\ 
-         Dinoflagellates & 2
-               & NC\_014287.1 & Durinskia baltica \\ [1ex]
-        %Entering sixth group
-         & & NC\_001603.2 & Euglena gracilis \\ 
-         Euglena & 2 & NC\_020018.1 & Monomorphina aenigmatica \\ [1ex]
-        %Entering seventh group
-         & & NC\_003386.1 & Psilotum nudum \\ 
-         & & NC\_008829.1 & Angiopteris evecta \\
-         Fern & 5 & NC\_014348.1 & Pteridium aquilinum \\ 
-         & & NC\_014699.1 & Equisetum arvense \\ 
-         & & NC\_017006.1 & Mankyua chejuensis \\ [1ex]
-         % Entering eighth group
-         & & NC\_007898.3 & Solanum lyopersicum \\
-         & & NC\_001568.1 & Epifagus virginiana \\ 
-         & & NC\_001666.2 & Zea Mays \\ 
-         & & NC\_005086.1 & Amborella trichopoda \\ 
-         & & NC\_006050.1 & Nymphaea alba \\ 
-         & & NC\_006290.1 & Panax ginseng \\ 
-         & & NC\_007578.1 & Lactuca sativa \\ 
-         & & NC\_007957.1 & vitis vinifera \\ 
-         & & NC\_007977.1 & Helianthus annuus \\ 
-         & & NC\_008325.1 & Daucus carota \\ 
-         & & NC\_008336.1 & Nandina domestica \\ 
-         & & NC\_008359.1 & Morus indica \\ 
-         & & NC\_008407.1 & Jasminum nudiflorum \\ 
-         & & NC\_008456.1 & Drimys granadensis \\ 
-         & & NC\_008457.1 & Piper cenocladum \\ 
-         & & NC\_009601.1 & Dioscorea elephantipes \\ 
-         & & NC\_009765.1 & Cuscuta gronovii \\ 
-         & & NC\_009808.1 & Ipomea purpurea \\ 
-        Angiosperms & 45 & NC\_010361.1 & Oenothera biennis \\ 
-         & & NC\_010433.1 & Manihot esculenta \\ 
-         & & NC\_010442.1 & Trachelium caeruleum \\ 
-         & & NC\_013707.2 & Olea europea \\ 
-         & & NC\_013823.1 & Typha latifolia \\ 
-         & & NC\_014570.1 & Eucalyptus \\ 
-         & & NC\_014674.1 & Castanea mollissima \\ 
-         & & NC\_014676.2 & Theobroma cacao \\ 
-         & & NC\_015830.1 & Bambusa emeiensis \\ 
-         & & NC\_015899.1 & Wolffia australiana \\ 
-         & & NC\_016433.2 & Sesamum indicum \\ 
-         & & NC\_016468.1 & Boea hygrometrica \\ 
-         & & NC\_016670.1 & Gossypium darwinii \\ 
-         & & NC\_016727.1 & Silene vulgaris \\ 
-         & & NC\_016734.1 & Brassica napus \\ 
-         & & NC\_016736.1 & Ricinus communis \\ 
-         & & NC\_016753.1 & Colocasia esculenta \\ 
-         & & NC\_017609.1 & Phalaenopsis equestris \\ 
-         & & NC\_018357.1 & Magnolia denudata \\ 
-         & & NC\_019601.1 & Fragaria chiloensis \\ 
-         & & NC\_008796.1 & Ranunculus macranthus \\ 
-         & & NC\_013991.2 & Phoenix dactylifera \\ 
-         & & NC\_016068.1 & Nicotiana undulata \\ [1ex]
-         %Entering ninth group
-         & & NC\_009618.1 & Cycas taitungensis \\ 
-         & & NC\_011942.1 & Gnetum parvifolium \\ 
-         & & NC\_016058.1 & Larix decidua \\ 
-         Gymnosperms & 7 & NC\_016063.1 & Cephalotaxus wilsoniana \\ 
-         & & NC\_016065.1 & Taiwania cryptomerioides \\ 
-         & & NC\_016069.1 & Picea morrisonicola \\ 
-         & & NC\_016986.1 & Gingko biloba \\ [1ex]
-         %Entering tenth group
-         Haptophytes & 1 & NC\_007288.1 & Emiliana huxleyi\\ [1ex]
-         %Entering eleventh group
-         Lycopodiophyta & 2 & NC\_014675.1 & Isoetes flaccida \\
-         & & NC\_006861.1 & Huperzia lucidula \\
-       \hline
-\end{longtable}
+      \parbox[t]{1mm}{\multirow{11}{*}{\rotatebox[origin=c]{90}{Brown Algae}}} &\multirow{11}{*}{11}  & NC\_001713.1 & Odontella sinensis \\ 
+      & & NC\_008588.1 & Phaeodactylum tricornutum \\ 
+      & & NC\_010772.1 & Heterosigma akashiwo \\ 
+      & & NC\_011600.1 & Vaucheria litorea \\ 
+      & & NC\_012903.1 & Aureoumbra lagunensis \\ 
+      &  & NC\_014808.1 & Thalassiosira oceanica \\ 
+      & & NC\_015403.1 & Fistulifera sp \\ 
+      & & NC\_016731.1 & Synedra acus \\ 
+      & & NC\_016735.1 & Fucus vesiculosus \\ 
+      & & NC\_018523.1 & Saccharina japonica \\ 
+      & & NC\_020014.1 & Nannochloropsis gadtina \\ 
+      \hline
+      % Entering second group
+      \parbox[t]{1mm}{\multirow{3}{*}{\rotatebox[origin=c]{90}{F1}}} &
+      \multirow{3}{*}{3} & NC\_000925.1 & Porphyra purpurea \\ 
+       &  & NC\_001840.1 & Cyanidium caldarium \\ 
+      & & NC\_006137.1 & Gracilaria tenuistipitata \\ 
+      \hline
+      % Entering third group
+      \parbox[t]{1mm}{\multirow{17}{*}{\rotatebox[origin=c]{90}{Green Algae}}} &
+      \multirow{17}{*}{17} & NC\_000927.1 & Nephroselmis olivacea \\ 
+      & & NC\_002186.1 & Mesotigma viride \\ 
+      & & NC\_005353.1 & Chlamydomonas reinhardtii \\ 
+      & & NC\_008097.1 & Chara vulgaris \\ 
+      & & NC\_008099.1 & Oltmannsiellopsis viridis \\ 
+      & & NC\_008114.1 & Pseudoclonium akinetum \\ 
+      & & NC\_008289.1 & Ostreococcus tauri \\ 
+      & & NC\_008372.1 & Stigeoclonium helveticum \\ 
+      & & NC\_008822.1 & Chlorokybus atmophyticus \\ 
+      & & NC\_011031.1 & Oedogonium cardiacum \\ 
+      & & NC\_012097.1 & Pycnococcus provaseolii \\ 
+      & & NC\_012099.1 & Pyramimonas parkeae \\ 
+      & & NC\_012568.1 & Micromonas pusilla \\ 
+      & & NC\_014346.1 & Floydiella terrestris \\ 
+      & & NC\_015645.1 & Schizomeris leibleinii \\ 
+      & & NC\_016732.1 & Dunaliella salina \\ 
+      & & NC\_016733.1 & Pedinomonas minor \\ % 
+      \hline
+      % Entering fourth group
+      \parbox[t]{1mm}{\multirow{3}{*}{\rotatebox[origin=c]{90}{F2}}} &
+      \multirow{3}{*}{3} & NC\_001319.1 & Marchantia polymorpha \\ 
+       &  & NC\_004543.1 & Anthoceros formosae \\ 
+      & & NC\_005087.1 & Physcomitrella patens \\ %
+      \hline
+      % Entering fifth group
+      \parbox[t]{1mm}{\multirow{2}{*}{\rotatebox[origin=c]{90}{F3}}} &
+      \multirow{2}{*}{2} & NC\_014267.1 & Kryptoperidinium foliaceum \\ 
+      & 
+      & NC\_014287.1 & Durinskia baltica \\ 
+      \hline
+
+      % Entering sixth group
+      \parbox[t]{1mm}{\multirow{2}{*}{\rotatebox[origin=c]{90}{F4}}}     &
+      \multirow{2}{*}{2} & NC\_001603.2 & Euglena gracilis \\ 
+      &  & NC\_020018.1 & Monomorphina aenigmatica \\ 
+       \hline
+       % Entering seventh group
+       \parbox[t]{1mm}{\multirow{5}{*}{\rotatebox[origin=c]{90}{Fern}}}     &       \multirow{5}{*}{5}
+       & NC\_003386.1 & Psilotum nudum \\ 
+      & & NC\_008829.1 & Angiopteris evecta \\
+      &  & NC\_014348.1 & Pteridium aquilinum \\ 
+      & & NC\_014699.1 & Equisetum arvense \\ 
+      & & NC\_017006.1 & Mankyua chejuensis \\ 
+      \hline
+    % Entering tenth group
+       & & & \\
+      \parbox[t]{1mm}{\multirow{1}{*}{\rotatebox[origin=c]{90}{F5}}}
+ & 1 & NC\_007288.1 & Emiliana huxleyi\\
+       & & & \\
+ \hline
+      % Entering eleventh group
+      \parbox[t]{1mm}{\multirow{2}{*}{\rotatebox[origin=c]{90}{F6}}}
+       & \multirow{2}{*}{2} & NC\_014675.1 & Isoetes flaccida \\
+      & & NC\_006861.1 & Huperzia lucidula \\
+      \hline
+ 
+
+    \end{tabular}
+  \end{minipage}    
+  \begin{minipage}{0.45\textwidth}
+   \begin{tabular}{|p{0.1cm}|p{0.1cm}|p{1.2cm}|p{2.7cm}|}
+      \hline
+      {{F.}}&{{\#}} & {{Acc. No}} & {{Scientific Name}} \\ 
+      \hline
+
+      % Entering eighth group
+      \parbox[t]{1mm}{\multirow{45}{*}{\rotatebox[origin=c]{90}{Angiosperms}}}  
+      & 
+      \multirow{45}{*}{45} & NC\_007898.3 & Solanum lyopersicum \\
+      & & NC\_001568.1 & Epifagus virginiana \\ 
+      & & NC\_001666.2 & Zea Mays \\ 
+      & & NC\_005086.1 & Amborella trichopoda \\ 
+      & & NC\_006050.1 & Nymphaea alba \\ 
+      & & NC\_006290.1 & Panax ginseng \\ 
+      & & NC\_007578.1 & Lactuca sativa \\ 
+      & & NC\_007957.1 & vitis vinifera \\ 
+      & & NC\_007977.1 & Helianthus annuus \\ 
+      & & NC\_008325.1 & Daucus carota \\ 
+      & & NC\_008336.1 & Nandina domestica \\ 
+      & & NC\_008359.1 & Morus indica \\ 
+      & & NC\_008407.1 & Jasminum nudiflorum \\ 
+      & & NC\_008456.1 & Drimys granadensis \\ 
+      & & NC\_008457.1 & Piper cenocladum \\ 
+      & & NC\_009601.1 & Dioscorea elephantipes \\ 
+      & & NC\_009765.1 & Cuscuta gronovii \\ 
+      & & NC\_009808.1 & Ipomea purpurea \\ 
+      & & NC\_010361.1 & Oenothera biennis \\ 
+      & & NC\_010433.1 & Manihot esculenta \\ 
+      & & NC\_010442.1 & Trachelium caeruleum \\ 
+      & & NC\_013707.2 & Olea europea \\ 
+      & & NC\_013823.1 & Typha latifolia \\ 
+      & & NC\_014570.1 & Eucalyptus \\ 
+      & & NC\_014674.1 & Castanea mollissima \\ 
+      & & NC\_014676.2 & Theobroma cacao \\ 
+      & & NC\_015830.1 & Bambusa emeiensis \\ 
+      & & NC\_015899.1 & Wolffia australiana \\ 
+      & & NC\_016433.2 & Sesamum indicum \\ 
+      & & NC\_016468.1 & Boea hygrometrica \\ 
+      & & NC\_016670.1 & Gossypium darwinii \\ 
+      & & NC\_016727.1 & Silene vulgaris \\ 
+      & & NC\_016734.1 & Brassica napus \\ 
+      & & NC\_016736.1 & Ricinus communis \\ 
+      & & NC\_016753.1 & Colocasia esculenta \\ 
+      & & NC\_017609.1 & Phalaenopsis equestris \\ 
+      & & NC\_018357.1 & Magnolia denudata \\ 
+      & & NC\_019601.1 & Fragaria chiloensis \\ 
+      & & NC\_008796.1 & Ranunculus macranthus \\ 
+      & & NC\_013991.2 & Phoenix dactylifera \\ 
+      & & NC\_016068.1 & Nicotiana undulata \\ 
+      \hline
+      % Entering ninth group
+      \parbox[t]{1mm}{\multirow{7}{*}{\rotatebox[origin=c]{90}{Gymnosperms}}}
+      & 
+      \multirow{7}{*}{7}& NC\_009618.1 & Cycas taitungensis \\ 
+      & & NC\_011942.1 & Gnetum parvifolium \\ 
+      & & NC\_016058.1 & Larix decidua \\ 
+      & & NC\_016063.1 & Cephalotaxus wilsoniana \\ 
+      & & NC\_016065.1 & Taiwania cryptomerioides \\ 
+      & & NC\_016069.1 & Picea morrisonicola \\ 
+      & & NC\_016986.1 & Gingko biloba \\ 
+      \hline
+     \end{tabular}
+  \end{minipage}
+ 
+  \scriptsize 
+  \noindent where families F1, F2, F3, F4, F5, and F6 are 
+  Red Algae,
+  Brypoytes, 
+  Dinoflagellates,
+  Euglena,
+  Haptophytes, and Lycopodiophyta respectively.
+
+  \normalsize
+  \caption[NCBI Genomes Families]{List of family groups of Chloroplast Genomes from NCBI\label{Tab2}}
+
+
+  \end{table}
 \end{center}  
-\end{tiny}
\ No newline at end of file
+