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  12 \@writefile{toc}{\contentsline {section}{\numberline {2}An Overview}{3}}
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  22 \@writefile{toc}{\contentsline {section}{\numberline {3}Core genes extraction}{4}}
  23 \@writefile{toc}{\contentsline {subsection}{\numberline {3.1}Similarity-based approach}{4}}
  24 \newlabel{sec:simil}{{3.1}{4}}
  25 \@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.1}Theoretical presentation}{4}}
  26 \@writefile{thm}{\contentsline {definition}{{Definition}{1}{}}{4}}
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  29 \@writefile{lot}{\contentsline {table}{\numberline {1}{\ignorespaces Size of core and pan genomes w.r.t. the similarity threshold, first and second approache.\relax }}{5}}
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  32 \@writefile{toc}{\contentsline {subsubsection}{\numberline {3.1.2}Case study}{6}}
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  35 \@writefile{toc}{\contentsline {subsection}{\numberline {3.2}Annotation based approach}{7}}
  36 \@writefile{toc}{\contentsline {subsubsection}{\numberline {3.2.1}Quality-test approach}{7}}
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  38 \@writefile{lof}{\contentsline {figure}{\numberline {2}{\ignorespaces Part of the implementation of the second method, compaire the common genes from NCBI and DOGMA.\relax }}{7}}
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  41 \@writefile{loa}{\contentsline {algorithm}{\numberline {1}{\ignorespaces Maximum similarity score between two sequences(geneChk)\relax }}{8}}
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  43 \@writefile{loa}{\contentsline {algorithm}{\numberline {2}{\ignorespaces Extract new genome based on gene quality test\relax }}{9}}
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  48 \newlabel{Etime}{{2}{9}}
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  55 \newlabel{subfig-2:pan}{{3b}{11}}
  56 \newlabel{sub@subfig-2:pan}{{(b)}{b}}
  57 \@writefile{lof}{\contentsline {figure}{\numberline {3}{\ignorespaces Sizes of Core and Pan genomes for first and second method.\relax }}{11}}
  58 \@writefile{lof}{\contentsline {subfigure}{\numberline{(a)}{\ignorespaces {Sizes of core genome}}}{11}}
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  65 \@writefile{lof}{\contentsline {figure}{\numberline {4}{\ignorespaces Gene comparisons cover from NCBI and DOGMA, second method\relax }}{11}}
  66 \@writefile{lof}{\contentsline {subfigure}{\numberline{(a)}{\ignorespaces {genes coverage of NCBI genomes}}}{11}}
  67 \@writefile{lof}{\contentsline {subfigure}{\numberline{(b)}{\ignorespaces {genes coverage of DOGMA genomes}}}{11}}
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  69 \@writefile{toc}{\contentsline {section}{\numberline {5}Discussion}{11}}
  70 \@writefile{toc}{\contentsline {subsection}{\numberline {5.1}Biological evaluation}{11}}
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  73 \@writefile{toc}{\contentsline {section}{\numberline {6}Conclusion}{12}}
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  75 \bibstyle{plain}
  76 \bibdata{biblio}
  77 \bibcite{acgs13:onp}{1}
  78 \bibcite{altschul1990basic}{2}
  79 \bibcite{apweiler1985swiss}{3}
  80 \bibcite{birney2004genewise}{4}
  81 \bibcite{de2002comparative}{5}
  82 \bibcite{Alkindy2014}{6}
  83 \bibcite{Bakke2009}{7}
  84 \bibcite{li2013complete}{8}
  85 \bibcite{Sayers01012011}{9}
  86 \bibcite{liu2012cpgavas}{10}
  87 \bibcite{guindon2005phyml}{11}
  88 \bibcite{mcfadden2001primary}{12}
  89 \bibcite{parra2000geneid}{13}
  90 \bibcite{parra2007cegma}{14}
  91 \bibcite{Rice2000}{15}
  92 \bibcite{RDOGMA}{16}
  93 \bibcite{stamatakis2008raxml}{17}
  94 \bibcite{stamatakis2005raxml}{18}
  95 \bibcite{sugawara2008ddbj}{19}