feat: Add a figure from Charles 2023 that represents the TAG definitions
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\caption[Tandemly Arrayed Genes (TAG) definitions]{
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Tandemly Arrayed Genes (TAG) definitions.
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% TAG definitions
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% Figure inspired from fig. 1 Charles 2023 internship report
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\documentclass[tikz]{standalone}
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\usepackage{tikz}
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\begin{document}
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\usetikzlibrary{positioning}
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\usetikzlibrary{decorations.pathreplacing}
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\tikzset{
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dot/.style={fill=black, circle, inner sep=1.5pt},
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nod/.style={sloped, at start, xshift=3mm, font=\scriptsize, above},
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}
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\begin{tikzpicture}[node distance=0.25]
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\newcommand{\geneLength}{1}
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\newcommand{\geneHalfHeight}{0.25}
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% DNA line
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\draw[-,very thick] (-6,0) to (6,0);
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% Gene blocks
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\node[rectangle,fill=orange,minimum height=0.5cm, minimum width=1cm] (orange1) at (-5,0) {};
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\node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green1) [right=of orange1] {};
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\node[rectangle,fill=red,minimum height=0.5cm, minimum width=1cm] (red1) [right=of green1] {};
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\node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green2) [right=of red1] {};
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\node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green3) [right=of green2] {};
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\node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green4) [right=of green3] {};
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\node[rectangle,fill=blue,minimum height=0.5cm, minimum width=1cm] (blue1) [right=of green4] {};
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\node[rectangle,fill=blue,minimum height=0.5cm, minimum width=1cm] (blue2) [right=of blue1] {};
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\node[rectangle,fill=orange,minimum height=0.5cm, minimum width=1cm] (orange2) [right=of blue2] {};
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% Homology links
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\draw[-,orange, bend left=40] (orange1) to coordinate[dot] node[nod] {$\mathrm{TAG}_7$} (orange2);
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\draw[-,green,bend right=40] (green1) to (green2)
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(green2) to (green3)
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(green3) to (green4);
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\draw[-,green,bend left=40] (green1) to (green3)
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(green1) to coordinate[dot] node[nod] {$\mathrm{TAG}_3$}(green4);
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\draw[-,green,bend right=40] (green1) to (green2)
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(green2) to (green4);
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\draw[-,blue, bend left=40] (blue1) to coordinate[dot] node[nod] {$\mathrm{TAG}_0$} (blue2);
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\end{tikzpicture}
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\end{document}
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@ -157,7 +157,13 @@ We apply a graph clustering algorithm on the graph in order to infer the gene fa
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FTAG Finder proposes three clustering algorithm alternatives: single linkage, Markov Clustering [cite:@vandongenNewClusterAlgorithm1998] or Walktrap [cite:@ponsComputingCommunitiesLarge2005].
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**** Detection of TAGs
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The final step of FTAG Finder consists in the identification of gls:TAG from the gene families and the positions of genes.
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For a given chromosome, the tool seeks genes belonging to the same family and located close to each other. The tool allows a maximal number of genes between the homologous genes, with a parameter set by the user.
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For a given chromosome, the tool seeks genes belonging to the same family and located close to each other. The tool allows a maximal number of genes between the homologous genes, with a parameter set by the user. Ref:fig:tag-definitions is a schematic representation of some possible gls:TAG positioning on a genome associated with their definition in FTAG Finder /Find Tags/ step.
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#+begin_export latex
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\fladdfig{
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\includegraphics[width=.9\linewidth]{./figures/tag-definition.pdf}
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\caption[Schematic representation of TAG definitions]{\label{fig:tag-definitions} Schematic representation of TAG definitions. Several genes are represented on a linear chromosome. The red box represent a singleton gene. Orange boxes represent a TAG with two duplicate genes seperated by 7 other genes ($\mathrm{TAG}_7$). Four green boxes constitute a TAG, the gene at the extremities are seperated by three genes ($\mathrm{TAG}_3$. The two blue boxes represents a TAG with two genes next to each other $\mathrm{TAG}_0$. The bended edges represents the homology links between each pair of genes of a TAG.}}
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#+end_export
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* Objectives for the internship
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** Scientific questions
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The underlying question of FTAG Finder is the study of the evolutionary fate of duplicate genes in Eukaryotes.
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BIN
report.pdf (Stored with Git LFS)
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report.pdf (Stored with Git LFS)
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