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

This commit is contained in:
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].
**** 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.
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
** Scientific questions
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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