feat: Add a figure from Charles 2023 that represents the TAG definitions

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Samuel Ortion 2024-04-16 15:15:28 +02:00
parent d1e898af47
commit bb191d4cf7
5 changed files with 63 additions and 3 deletions

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\caption[Tandemly Arrayed Genes (TAG) definitions]{
Tandemly Arrayed Genes (TAG) definitions.
}

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figures/tag-definition.pdf (Stored with Git LFS) Normal file

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% TAG definitions
% Figure inspired from fig. 1 Charles 2023 internship report
\documentclass[tikz]{standalone}
\usepackage{tikz}
\begin{document}
\usetikzlibrary{positioning}
\usetikzlibrary{decorations.pathreplacing}
\tikzset{
dot/.style={fill=black, circle, inner sep=1.5pt},
nod/.style={sloped, at start, xshift=3mm, font=\scriptsize, above},
}
\begin{tikzpicture}[node distance=0.25]
\newcommand{\geneLength}{1}
\newcommand{\geneHalfHeight}{0.25}
% DNA line
\draw[-,very thick] (-6,0) to (6,0);
% Gene blocks
\node[rectangle,fill=orange,minimum height=0.5cm, minimum width=1cm] (orange1) at (-5,0) {};
\node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green1) [right=of orange1] {};
\node[rectangle,fill=red,minimum height=0.5cm, minimum width=1cm] (red1) [right=of green1] {};
\node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green2) [right=of red1] {};
\node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green3) [right=of green2] {};
\node[rectangle,fill=green,minimum height=0.5cm, minimum width=1cm] (green4) [right=of green3] {};
\node[rectangle,fill=blue,minimum height=0.5cm, minimum width=1cm] (blue1) [right=of green4] {};
\node[rectangle,fill=blue,minimum height=0.5cm, minimum width=1cm] (blue2) [right=of blue1] {};
\node[rectangle,fill=orange,minimum height=0.5cm, minimum width=1cm] (orange2) [right=of blue2] {};
% Homology links
\draw[-,orange, bend left=40] (orange1) to coordinate[dot] node[nod] {$\mathrm{TAG}_7$} (orange2);
\draw[-,green,bend right=40] (green1) to (green2)
(green2) to (green3)
(green3) to (green4);
\draw[-,green,bend left=40] (green1) to (green3)
(green1) to coordinate[dot] node[nod] {$\mathrm{TAG}_3$}(green4);
\draw[-,green,bend right=40] (green1) to (green2)
(green2) to (green4);
\draw[-,blue, bend left=40] (blue1) to coordinate[dot] node[nod] {$\mathrm{TAG}_0$} (blue2);
\end{tikzpicture}
\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
FTAG Finder proposes three clustering algorithm alternatives: single linkage, Markov Clustering [cite:@vandongenNewClusterAlgorithm1998] or Walktrap [cite:@ponsComputingCommunitiesLarge2005]. FTAG Finder proposes three clustering algorithm alternatives: single linkage, Markov Clustering [cite:@vandongenNewClusterAlgorithm1998] or Walktrap [cite:@ponsComputingCommunitiesLarge2005].
**** Detection of TAGs **** Detection of TAGs
The final step of FTAG Finder consists in the identification of gls:TAG from the gene families and the positions of genes. The final step of FTAG Finder consists in the identification of gls:TAG from the gene families and the positions of genes.
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. 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.
#+begin_export latex
\fladdfig{
\includegraphics[width=.9\linewidth]{./figures/tag-definition.pdf}
\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.}}
#+end_export
* Objectives for the internship * Objectives for the internship
** Scientific questions ** Scientific questions
The underlying question of FTAG Finder is the study of the evolutionary fate of duplicate genes in Eukaryotes. The underlying question of FTAG Finder is the study of the evolutionary fate of duplicate genes in Eukaryotes.

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report.pdf (Stored with Git LFS)

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