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\documentstyle{Feb 6 Update}  \begin{document}  \section*{Orthologs} \section*{Feb 6 Update}   \subsection*{Orthologs}  \begin{verbatim}  I have all of the orthologs mouse to zebrafish orthologs for a while. Recently I did  a bit of processing and narrowed the list down to just one to one orthologs since  that seems to be what the Clark paper wants.  \end{verbatim}  \subsection*{Paralogs}   \begin{verbatim}   This is the section I have had the most issues with. I initially relied on a fetch all paralogs   method from ensembl but that cut out before it was done. So I went in and pulled paralogs for each   unchecked gene individually, thinking that I would add this new set to my pre-existing set. There   were two issues with that idea that I discovered recently. Firstly, that method also was interrupted   prematurely by the server cutting my connection. Secondly, and more dire, this gene based paralog fetching   seems to pull far more paralogs per gene. That worries me, since I want a consistent method of evaluating   what is and what is no a paralog. Currently I am running a test script that should allow me to limit   paralogs to only the most highly related pair.   \end{verbatim}   \subsection*{Annotations}   \begin{verbatim}   I used the Gene Ontology website to get their annotation guide and the annotations for   mice and zebrafish. I also went through the annotation and selected for only those annotations   that experimental support and focus on the processes outlined in the clark paper.   \end{verbatim}   \subsection*{General Work}   \begin{verbatim}   There has been a lot of hurry up and wait for a long time so I've been trying to prep myself for   future steps while I wait for programs to finish. There has been a lot of learning and relearning   Ensembl's API. I have also been learning python and practicing with it for when I get the scripts.   I also have been reading papers on Phenoscape and Phenex and am starting the process of learning all   the languages and API's I'll need to work with Phenoscape.   \end{verbatim}  \end{document}