rephrase and switch back to link all toc entries, but uncolored
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921b5821a2
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2110e31754
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report.org
28
report.org
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@ -9,13 +9,8 @@
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#+exclude_tags: noexport
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#+exclude_tags: noexport
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#+options: H:7
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#+options: H:7
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#+options: toc:nil
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#+options: toc:nil
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#+MACRO: conditional-header (eval (concat "#+header: :results output " (print-to-string org-export-current-backend)))
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# ref. conditional-header https://emacs.stackexchange.com/a/64340/41374
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# ref. https://write.as/dani/writing-a-phd-thesis-with-org-mode
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# ref. https://write.as/dani/writing-a-phd-thesis-with-org-mode
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#+name: acronyms
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#+name: acronyms
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| key | abbreviation | full form |
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| key | abbreviation | full form |
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|------------+--------------+--------------------------------------------|
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|------------+--------------+--------------------------------------------|
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@ -53,9 +48,12 @@
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#+end_center
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#+end_center
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#+begin_export latex
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#+begin_export latex
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{
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\hypersetup{linkcolor=black}
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\tableofcontents
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\tableofcontents
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\listoffigures
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\listoffigures
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\listoftables
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\listoftables
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}
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#+end_export
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#+end_export
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[[printglossaries:]]
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[[printglossaries:]]
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@ -154,19 +152,21 @@ In this step, the typical tool involved is =BLAST= (Basic Local Alignment Search
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Several =BLAST= metrics can be used as an homology measure, such as bitscore, identity percentage, E-value or variations of these. The choice of metrics can affect the results of graph clustering in the following step, and we should therefore chose them carefully [cite:@gibbonsEvaluationBLASTbasedEdgeweighting2015].
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Several =BLAST= metrics can be used as an homology measure, such as bitscore, identity percentage, E-value or variations of these. The choice of metrics can affect the results of graph clustering in the following step, and we should therefore chose them carefully [cite:@gibbonsEvaluationBLASTbasedEdgeweighting2015].
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**** Identification of gene families
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**** Identification of gene families
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Based on the homology links between each pair of genes, we construct a undirected weighted graph whose vertices correspond to genes and edges to homology links between them.
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Based on the homology links between each pair of genes, we construct an undirected weighted graph whose vertices correspond to genes and edges to homology links between them.
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We apply a graph clustering algorithm on the graph in order to infer the gene families corresponding to densely connected communities of vertices.
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We apply a graph clustering algorithm on the graph in order to infer the gene families corresponding to densely connected communities of vertices.
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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. 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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#+begin_export latex
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\fladdfig{
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\fladdfig{
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\includegraphics[width=.9\linewidth]{./figures/tag-definition.pdf}
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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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\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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#+end_export
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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. Cref: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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* Objectives for the internship
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* Objectives for the internship
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** Scientific questions
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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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The underlying question of FTAG Finder is the study of the evolutionary fate of duplicate genes in Eukaryotes.
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@ -216,6 +216,10 @@ Principle: construct vertex communities based on where an agent would get stuck
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# LocalWords: speciation Subfunctionalization Neofunctionalization
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# LocalWords: speciation Subfunctionalization Neofunctionalization
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# LocalWords: Pseudogenization
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# LocalWords: Pseudogenization
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# Local Variables:
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# eval: (progn (org-babel-goto-named-src-block "startup") (org-babel-execute-src-block) (outline-hide-sublevels 1))
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# End:
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* Setup :noexport:
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* Setup :noexport:
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#+name: startup
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#+name: startup
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@ -225,7 +229,3 @@ Principle: construct vertex communities based on where an agent would get stuck
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#+RESULTS: startup
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#+RESULTS: startup
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: Loaded ./setup.el
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: Loaded ./setup.el
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# Local Variables:
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# eval: (progn (org-babel-goto-named-src-block "startup") (org-babel-execute-src-block) (outline-hide-sublevels 1))
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# End:
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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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@ -84,7 +84,7 @@
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linkcolor=primaryLink,
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linkcolor=primaryLink,
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anchorcolor=primaryLink,
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anchorcolor=primaryLink,
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citecolor=primaryCite,
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citecolor=primaryCite,
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linktoc=page
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%linktoc=page
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}
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}
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\newcommand*{\glsplainhyperlink}[2]{%
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\newcommand*{\glsplainhyperlink}[2]{%
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\begingroup%
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\begingroup%
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