deletions | additions       diff --git a/Feb 6 Update.tex b/Feb 6 Update.tex  index d9d8ee9..9e40086 100644  --- a/Feb 6 Update.tex  +++ b/Feb 6 Update.tex 
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\section*{Feb 6 Update}  \subsection*{Orthologs}  \begin{verbatim}  I have had  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. This was done using editOrtholgs.pl. I removed  that change but kept the script just in case it, or something like it, needs to be done again.  \end{verbatim}  \subsection*{Paralogs}  \begin{verbatim} 
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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 not a paralog. Currently I am running a test script that should allow me to limit  paralogs to only the most highly related pair. That script, zebraTopInParalogs.pl, was tested and works  but it has proved unnessecary. Moreover, the fetch by gene method used in ___paralogsExtra.pl returns the  same paralog sets as the fetch all method used in ___paralogs.pl. This was verified by spot checking with  several genes pulled from the fetch all method.  \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. paper, using   clean___Ontology.pl. All of this data and the scripts are stored in my Ontology folder.  \end{verbatim}  \subsection*{General Work}  \begin{verbatim}