  <SECT2 ID="DISPLAYMENU-GC-CONTENT">
    <TITLE>GC Content (%)</TITLE>
    <PARA>
Controls whether the GC content plot is visible.  This is a graph of the
average GC content of a moving window (default size 120 base), across the
bases visible in the overview window.
[Default: off] [short name: <LITERAL>gc_content</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-GCSD-CONTENT">
    <TITLE>GC Content (%) With 2.5 SD Cutoff</TITLE>
    <PARA>
Controls whether the cutoff GC content plot is visible.  This is similar to
the GC content graph, but the plot is clipped so that the GC content of each
algorithm window is shown only when it is more than 2.5 times the standard
deviation of the GC content in all the windows.
[Default: off] [short name: <LITERAL>sd_gc_content</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-AG-CONTENT">
    <TITLE>AG Content (%)</TITLE>
    <PARA>
Controls whether the AG content plot is visible.  This is a graph of the
average AG content of a moving window (default size 120 base), across the
bases visible in the overview window.
[Default: off] [short name: <LITERAL>ag_content</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-GC-FRAME-PLOT">
    <TITLE>GC Frame Plot</TITLE>
    <PARA>
Controls whether the GC frame plot is visible.  This graph is similar to the
GC content graph but shows the GC content of the first, second and third
position independently.  For more information on the algorithm and on how to
interpret the result see <ULINK
URL="http://www.nih.go.jp/~jun/cgi-bin/frameplot.pl" TYPE="external">this web
page</ULINK>.
[Default: off] [short name: <LITERAL>gc_frame</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-CORRELATION-SCORES">
    <TITLE>Correlation Scores</TITLE>
    <PARA>
Controls whether the (forward) correlation scores plot is visible.  The graph
shows the correlation between the amino acid composition of the globular
proteins in TREMBL and the composition of the base translation in each of the
three reading frames.  The green line represents forward frame 1, blue
represents frame 2 and red represents frame 3.
[Default: off] [short name: <LITERAL>correlation_score</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-REVERSE-CORRELATION-SCORES">
    <TITLE>Reverse Correlation Scores</TITLE>
    <PARA>
This does the same as "Correlation Scores", but does the calculation on the
reverse strand.  The green line represents reverse frame 1 (the bottom frame
line), blue represents frame 2 and red represents frame 3.
[Default: off] [short name: <LITERAL>correlation_score</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-GC-DEVIATION">
    <TITLE>GC Deviation (G-C)/(G+C)</TITLE>
    <PARA>
Controls whether the GC deviation plot is visible.  This graph shows the
difference between the "G" content of the forward strand and the reverse
strand.
[Default: off] [short name: <LITERAL>gc_deviation</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-AT-DEVIATION">
    <TITLE>AT Deviation (A-T)/(A+T)</TITLE>
    <PARA>
Controls whether the AT deviation plot is visible.  This graph shows the
difference between the "A" content of the forward strand and the reverse
strand.
[Default: off] [short name: <LITERAL>at_deviation</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-KARLINSIG">
    <TITLE>Karlin Signature Difference</TITLE>
    <PARA>
This menu item toggles the display of the graph of the dinucleotide absolute
relative abundance difference between the whole sequence and a sliding window.
    </PARA>
    <PARA>
For details of the algorithm see "Global dinucleotide signatures and analysis
of genomic heterogeneity" Samuel Karlin - <ULINK
URL="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=10066522&amp;dopt=Abstract">Current
Opinion in Microbiology 1998, 1:598-610</ULINK>.
[Default: off] [short name: <LITERAL>karlin_sig</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-CUMULATIVEAT">
    <TITLE>Cumulative AT Skew, (A-T)/(A+T) and Cumulative GC Skew, (G-C)/(G+C)</TITLE>
    <PARA>
       Grigoriev A (1999)  Strand-specific compositional asymmetries in 
       double-stranded DNA viruses. Virus Research 60, 1-19.
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-POSITIONALASYM">
    <TITLE>Positional Asymmetry</TITLE>
    <PARA>
       Shulman MJ, Steinberg CM, Westmoreland N (1981) The coding function of 
       nucleotide sequences can be discerned by statistical analysis. J Theor Biol 
       88:409-20
    </PARA>
  </SECT2>

   <SECT2 ID="DISPLAYMENU-ENTROPY">
    <TITLE>Informational Entropy</TITLE>
    <PARA>
       Konopka A (1984) Is the information content of DNA evolutionarily 
       significant? J Theor Biol 107:697-704
    </PARA>
  </SECT2>
 
  <SECT2 ID="DISPLAYMENU-SCALEDCHISQ">
    <TITLE>Scaled Chi Square</TITLE>
    <PARA>
      Shields DC, Sharp PM (1987) Synonymous codon usage in Bacillus subtilis 
      reflects both translational selection and mutational biases. Nucleic Acids 
      Res 15:8023-40
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-MUTRES">
    <TITLE>Mutational Response Index</TITLE>
    <PARA>
      Gatherer D, McEwan NR (1997) Small regions of preferential codon usage and 
      their effect on overall codon bias--the case of the plp gene. Biochem Mol 
      Biol Int 43:107-14
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-NC">
    <TITLE>Effective Codon Number</TITLE>
    <PARA>
      Wright F (1990) The 'effective number of codons' used in a gene. Gene 87:23-9
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-INTRINSIC">
    <TITLE>Intrinsic Codon Deviation Index</TITLE>
    <PARA>
      Freire-Picos MA, Gonzalez-Siso MI, Rodriguez-Belmonte E, Rodriguez-Torres 
      AM, Ramil E, Cerdan ME (1994) Codon usage in Kluyveromyces lactis and in 
      yeast cytochrome c-encoding genes. Gene 139:43-9
    </PARA>
  </SECT2>

