menus.sgml

Remove each selected feature from it's entry.
[shortcut key: control-delete]
    </PARA>
  </SECT3>

  <SECT3 ID="DELETE-SELECTED-EXONS">
    <TITLE>Delete Exons</TITLE>
    <PARA>
Delete the selected exons.  The last exon of a feature can't be deleted
(delete the whole feature instead).
    </PARA>
  </SECT3>

  <SECT3 ID="DELETE-SELECTED-INTRONS">
    <TITLE>Remove Introns</TITLE>
    <PARA>
Delete the selected introns.
    </PARA>
  </SECT3>
  </SECT2>


  <SECT2 ID="EDITMENU-MOVE-SELECTED-FEATURES">
    <TITLE>Move Selected Features To</TITLE>
    <PARA>
Move the selected features to another entry.  Choose the destination entry
from the sub-menu.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-COPY-SELECTED-FEATURES">
    <TITLE>Copy Selected Features To</TITLE>
    <PARA>
Copy the selected features to another entry.  Choose the destination entry
from the sub-menu.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-TRIM">
   <TITLE>Trim Selected Features</TITLE>
  <SECT3 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-MET">
    <TITLE>To Met</TITLE>
    <PARA>
For each of the selected features this function will attempt to move the start
position to the first ATG in the feature if the feature does not already start
on a ATG codon.  If there is no ATG in the first thirty percent of the bases
of the feature the start position will be unchanged.  The search will stop at
the end of the first segment of a multi-segment feature.
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-ANY">
    <TITLE>To Any</TITLE>
    <PARA>
This works in the same way as "Trim Selected Features To Met", but will
attempt to move the start position of the feature to the first TTG, ATG or GTG
in the feature if it does not already start on one of those codons.  As above
it will only search the first thirty percent of the feature bases and will
only search the first segment of a multi-segment feature.
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-NEXT-MET">
    <TITLE>To Next Met</TITLE>
    <PARA>
For each of the selected features this function will attempt to move the start
position to the next ATG in the feature (the first codon is skipped).  If
there is no ATG in the first thirty percent of the bases of the feature the
start position will be unchanged.  The search will stop at the end of the
first segment of a multi-segment feature.
[shortcut key: T]
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-TRIM-SELECTED-FEATURES-TO-NEXT-ANY">
    <TITLE>To Next Any</TITLE>
    <PARA>
This works in the same way as "Trim Selected Features To Next Met", but will
attempt to move the start position of the feature to the next TTG, ATG or GTG
in the feature (the first codon is skipped).  As above it will only search the
first thirty percent of the feature bases and will only search the first
segment of a multi-segment feature.
[shortcut key: Y]
    </PARA>
  </SECT3>
  </SECT2>

  <SECT2 ID="EDITMENU-EXTEND">
    <TITLE>Extend Selected Features</TITLE>
  <SECT3 ID="EDITMENU-EXTEND-TO-PREVIOUS-STOP-CODON">
    <TITLE>To Previous Stop Codon</TITLE>
    <PARA>
Extend each of the selected features which do not start on a stop codon so
that each feature starts just after the previous stop codon in this reading
frame.
[shortcut key: Q]
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-EXTEND-TO-NEXT-STOP-CODON">
    <TITLE>To Next Stop Codon</TITLE>
    <PARA>
Extend each of the selected features which do not end on a stop codon so that
each feature ends just before the next stop codon in this reading frame.
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-EXTEND-TO-NEXT-STOP-CODON-FIX">
    <TITLE>To Next Stop Codon and Fix</TITLE>
    <PARA>
Same as above but in addition this fixes the stop codons.
    </PARA>
  </SECT3>

  </SECT2>

  <SECT2 ID="EDITMENU-FIX-STOP-CODONS">
    <TITLE>Fix Stop Codons</TITLE>
    <PARA>
Check and fix the stop codons to all the selected features.  For each feature
if the last codon is a stop codon, then all is well, nothing further is done
to the feature.  If the last codon is not a stop codon, but the very next
codon is a stop codon, then the end of the feature is moved forward by three
bases.  If both the last codon and the very next codon after the feature are
not stop codons, the feature is selected, an error message is displayed and
processing stops immediately.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-AUTO-GENE-NAMES">
    <TITLE>Automatically Create Gene Names</TITLE>
    <PARA>
Ask for a gene name prefix (using a text requester), and then give a unique
gene name to each CDS feature in the active entries using that prefix.  For
example if there are four CDS features with locations:
"<LITERAL>1..500</LITERAL>", "<LITERAL>complement(100..600)</LITERAL>",
"<LITERAL>200..700</LITERAL>" and "<LITERAL>complement(300..800)</LITERAL>",
entering <LITERAL>SPBC16A3</LITERAL> will give the four features these names:
<LITERAL>SPBC16A3.01</LITERAL>, <LITERAL>SPBC16A3.02c</LITERAL>,
<LITERAL>SPBC16A3.03</LITERAL> and <LITERAL>SPBC16A3.04c</LITERAL>.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-FIX-GENE-NAMES">
    <TITLE>Fix Gene Names</TITLE>
    <PARA>
For each selected CDS, add the gene name from the CDS to
neighbouring/overlapping mRNA, intron, exon, gene, 5'UTR and 3'UTR features.
Warn about inconsistencies such as overlapping CDSs.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-BASES">
    <TITLE>Bases</TITLE>
  <SECT3 ID="EDITMENU-REVERSE-AND-COMPLEMENT">
    <TITLE>Reverse And Complement</TITLE>
    <PARA>
Reverse and complement the sequence and all the features in all the entries
(active and inactive).
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-REVERSE-AND-COMPLEMENT-CONTIG"> 
    <TITLE>Reverse And Complement Selected Contig</TITLE>
    <PARA>
Reverse and complement the sequence and all the features in a selected 
contig feature. If this option is used in ACT then all the matches within the contig are
also reversed. Any matches extending past the boundary of the contig are
deleted. The changes to the comparison file can be saved by right clicking
in the comparison window and selecting "Save Comparison File...". However,
ideally the comparison between the two sequences should be recalculated.
    </PARA>
  </SECT3>


  <SECT3 ID="EDITMENU-DELETE-SELECTED-BASES">
    <TITLE>Delete Selected Bases</TITLE>
    <PARA>
Deletes the selected range of bases (if any) from both strands.  The deletion
will not proceed if the selected range overlaps any features.
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-ADD-BASES-AT-SELECTION">
    <TITLE>Add Bases At Selection</TITLE>
    <PARA>
Prompt the user for some bases to insert just before the selected bases.  The
operation will not proceed if there is no selected range, but bases can be
inserted anywhere in the sequence, including inside a feature.  The same
bases, reversed and complemented, will be inserted at the corresponding place
on the opposite strand.
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-ADD-FROM-FILE">
    <TITLE>Add Bases From File ...</TITLE>
    <PARA>
Prompt the user for the name of a file containing the bases to insert just
before the selected bases.
    </PARA>
  </SECT3>

  <SECT3 ID="EDITMENU-REPLACE-BASES-AT-SELECTION">
    <TITLE>Replace Bases At Selection</TITLE>
    <PARA>
Prompt the user for some bases to replace the selected bases.
    </PARA>
  </SECT3>

  </SECT2>

  <SECT2 ID="EDITMENU-CONTIG-REORDERING">
    <TITLE>Contig Reordering ...</TITLE>
    <PARA>
Opens a 'Contig Tool' displaying contigs, i.e. with feature keys 'fasta_record'
or 'contig'. The former being created automatically for each sequence when a 
mutiple fasta sequence file is read in. The contigs in this tool can then individually 
be selected and dragged and dropped to another location. In this way the order
of contigs and features within a contig can be changed. 
    </PARA>
    <PARA>
If this is used in ACT then the matches are also reordered with respect to the 
change in the sequence. If a match spans the boundary of a contig that is being
moved then if possible it is split. In some situations where there is a match
with 'indels' then this is not possible and the match is deleted. The changes to 
the comparison file can be saved by right clicking in the comparison window and 
selecting "Save Comparison File...". However, ideally the comparison between the 
two sequences should be recalculated.
    </PARA>
  </SECT2>

  <SECT2 ID="EDITMENU-EDIT-HEADER">
    <TITLE>Header Of Default Entry</TITLE>
    <PARA>
Open a edit window containing the header of the default entry.  Changes made
in the edit window will be applied immediately to the entry provided there are
no errors in the formatting of the header.
    </PARA>
  </SECT2>

</SECT1>

<SECT1 ID="CREATEMENU">
  <TITLE>The Create Menu</TITLE>
  <PARA>
This menu contains functions for creating new features (see <XREF
LINKEND="CONCEPTS-FEATURE">) or entries (see <XREF LINKEND="CONCEPTS-ENTRY">).
  </PARA>

  <SECT2 ID="CREATEMENU-NEW-FEATURE">
    <TITLE>New Feature</TITLE>
    <PARA>
Create a new feature in the default entry with a key of "misc_feature" (see
<XREF LINKEND="CONCEPTS-KEY">), a location of that spans the whole sequence
and which has no qualifiers (see <XREF LINKEND="CONCEPTS-QUALIFIERS">).
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-CREATE-FEATURE-FROM-BASE-RANGE">
    <TITLE>Feature From Base Range</TITLE>
    <PARA>
Create a new feature in the default entry with a key of "misc_feature", no
qualifiers and a location that exactly matches the selected range of bases.
If no bases are selected an error will be reported.
[shortcut key: C]
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-CREATE-INTERGENIC-FEATURES">
    <TITLE>Intergenic Features</TITLE>
    <PARA>
Create new features between CDS features in the default entry all with the "misc_feature" key.
    </PARA>
  </SECT2>


  <SECT2 ID="CREATEMENU-CREATE-FEATURES-FROM-NON-MATCHING-REGIONS">
    <TITLE>Features From Non-matching Regions</TITLE>
    <PARA>
Create features in ACT spanning all the regions where a match is not to be
found.
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-NEW-ENTRY">
    <TITLE>New Entry</TITLE>
    <PARA>
Create a new entry with no name and no features.  The new entry will become
the default entry (see <XREF LINKEND="CONCEPTS-DEFAULTENTRY">).
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-MARK-ORF">
    <TITLE>Mark Open Reading Frames ...</TITLE>
    <PARA>
Create a feature for each "large" open reading frame in the sequence.  The
default minimum size of a "large" open reading frame can be changed by
changing the <LITERAL>minimum_orf_size</LITERAL> option (see <XREF
LINKEND="OPTIONS-MIN-ORF-SIZE">).  If a codon usage file (see <XREF
LINKEND="GRAPHMENU-USAGE-PLOTS">) has been read each new ORF will have a codon
usage score added as a /score qualifier.  The new features can then be
filtered from the display (see "Set Score Cutoffs ..." in <XREF
LINKEND="VIEWS-POPUPMENU">).
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-MARK-EMPTY-ORFS">
    <TITLE>Mark Empty ORFs ...</TITLE>
    <PARA>
Create a feature for each open reading frame that doesn't already contain a
feature.
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-MARK-ORF-IN-RANGE">
    <TITLE>Mark Open Reading Frames In Range ...</TITLE>
    <PARA>
Create a feature for each "large" open reading frame in a range of bases.  A
range must be selected before using this command.
    </PARA>
  </SECT2>

  <SECT2 ID="CREATEMENU-MARK-FROM-PATTERN">
    <TITLE>Mark From Pattern ...</TITLE>
    <PARA>
Open a text requester to ask the user for a base pattern, then create a
feature for each group of bases that matches that pattern.  A new entry will
be created to hold the features with the name "matches: &lt;pattern&gt;",
where &lt;pattern&gt; is the pattern that was entered be the user.  Any IUB
base code can be used in the pattern, so for example, aanntt will match any
six bases that start with "aa" and ends with "tt".
    </PARA>
    <PARA>
      <TABLE COLSEP="1" FRAME="all" ROWSEP="1" ID="IUB-BASE-CODES">
        <TITLE>IUB Base Codes</TITLE>
        <TGROUP COLS="3" CHAROFF="50">
          <COLSPEC COLNUM="1" ALIGN="left">
          <COLSPEC COLNUM="2" ALIGN="left">
          <COLSPEC COLNUM="3" ALIGN="left">
          <TBODY>
          <ROW>
            <ENTRY>R = A or G</ENTRY>
            <ENTRY>S = G or C</ENTRY>
            <ENTRY>B = C, G or T</ENTRY>
          </ROW>
          <ROW>
            <ENTRY>Y = C or T</ENTRY>
            <ENTRY>W = A or T</ENTRY>
            <ENTRY>D = A, G or T</ENTRY>
          </ROW>
          <ROW>
            <ENTRY>K = G or T</ENTRY>
            <ENTRY>N = A, C, G or T</ENTRY>
            <ENTRY>H = A, C or T</ENTRY>
          </ROW>
          <ROW>
            <ENTRY>M = A or C</ENTRY>
            <ENTRY></ENTRY>
            <ENTRY>V = A, C or G</ENTRY>
          </ROW>
          </TBODY>
        </TGROUP>
      </TABLE>
    </PARA>
   </SECT2>

  <SECT2 ID="CREATEMENU-MARK-AMBIGUITIES">
    <TITLE>Mark Ambiguities</TITLE>
    <PARA>
Create a new feature for each block of ambiguous bases.  The new features will
have a key of <LITERAL>misc_feature</LITERAL> and will created in a new entry
called "ambiguous bases".
    </PARA>
  </SECT2>
</SECT1>

<SECT1 ID="RUNMENU">
  <TITLE>The Run Menu</TITLE>
  <PARA>
This menu is primarily used for running external programs on UNIX.
Additionally there are menu options to send sequences from selected
features to the <ULINK URL="http://blast.ncbi.nlm.nih.gov/Blast.cgi"
TYPE="external">NCBI web BLAST</ULINK> and <ULINK URL="http://pfam.sanger.ac.uk/"
TYPE="external">Pfam</ULINK>.
  </PARA>
  <PARA>
Once configured correctly, running an external
program should be as simple as selecting some features of interest, then
choosing one of the items from the run menu.  When the external programs
finishes the results can viewed using the "Search Results" item in the View
menu (see <XREF LINKEND="VIEWMENU-SEARCH-RESULTS">).
  </PARA>
  <SECT2 ID="RUNMENU-CONFIGURATION">
    <TITLE>Configuring the Run Menu</TITLE>
    <PARA>
To use this feature the <LITERAL>run_blastp</LITERAL>,
<LITERAL>run_fasta</LITERAL>  etc. scripts that are supplied
with &prog; will need to be changed to reflect the paths and databases that
are configured at each site.  Note that the <LITERAL>run</LITERAL> scripts are
stored in the <LITERAL>etc/</LITERAL> directory.
    </PARA>
    <PARA>
Each external program that is listed in the options file (see <XREF
LINKEND="OPTIONS-FEATURE-DNA-PROGRAMS"> and <XREF
LINKEND="OPTIONS-FEATURE-PROTEIN-PROGRAMS">) gets a "run" menu item and a "set
options" menu item.  For each external program (such as blastp) there must be
a shell script available that sets any necessary environment variables and
then launches the search/analysis program (for blastp
the script is called <LITERAL>run_blastp</LITERAL>).
    </PARA>
    <PARA>
Taking blastp as an example, this is the sequence of events that occurs when
the user selects the "Run blastp on selected features" menu item:
      <ORDEREDLIST>
        <LISTITEM>
          <PARA>
&prog; creates a new directory in the current directory called blastp.
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
A protein FASTA sequence file is written in the new directory for each
selected feature.  (For a DNA search program such as blastn the file will be a
DNA FASTA file).  The sequence file name will be something like:
<LITERAL>blastp/features.tab.seq.00001</LITERAL>.
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
The name of the expected output file is stored in the feature in a qualifier
called <LITERAL>/blastp_file</LITERAL>.  If the entry is called
<LITERAL>features.tab</LITERAL> then the qualifier will be set to something
like: <LITERAL>/blastp_file="blastp/features.tab.seq.00001.out"</LITERAL>.
Note that because the file name is stored in the entry you will need to save
the entry to keep the association between the features and the output files.
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
A file is then written (called something like
<LITERAL>blastp/file_of_filenames.1</LITERAL>) that contains the names of all
the newly created sequence files in the blastp directory.
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
&prog then tries to read the <LITERAL>run_blastp</LITERAL> script from the
&prog; installation directory.  The script is executed like this:
          </PARA>
          <PARA>
<LITERAL>run_blastp blastp/file_of_filenames.1 [options]</LITERAL>
          </PARA>
          <PARA>
where <LITERAL>[options]</LITERAL> currently must be a single word (normally a
database to search).  In the case of blastp/blastn/fasta etc. the second
argument of the script is passed directly to the blast/fasta as the database
name.  For testing purposes it is possible to run <LITERAL>run_blastp</LITERAL>
on the command line with the same arguments as above.
          </PARA>
          <PARA>
<LITERAL>run_blastp</LITERAL> will run blastp on each of the sequence files
listed in <LITERAL>file_of_filenames.blastp</LITERAL> and save the output
in the corresponding <LITERAL>.out</LITERAL> file.
          </PARA>
        </LISTITEM>
        <LISTITEM>
          <PARA>
If the program is successfully started, control will immediately return to the
user.  When <LITERAL>run_blastp</LITERAL> finishes a message will be
displayed to alert the user.
          </PARA>
          <PARA>
If necessary, it is possible to exit once &prog; indicates that the external
program has been started and the entry has been saved.
<LITERAL>run_blastp</LITERAL> will keep running in the background.
          </PARA>
        </LISTITEM>
      </ORDEREDLIST>
    </PARA>
  </SECT2>
</SECT1>

<SECT1 ID="GRAPHMENU">
  <TITLE>The Graph Menu</TITLE>
  <PARA>
Some general information about the graphs can be found in <XREF
LINKEND="GRAPHS">.  Configuration options for graphs are described in <XREF
LINKEND="OPTIONS-PLOTS">.
  </PARA>
  <SECT2 ID="GRAPHMENU-HIDE-ALL-GRAPHS">
    <TITLE>Hide All Graphs</TITLE>
    <PARA>
This item will turn off all the visible graphs.
    </PARA>
  </SECT2>

  <SECT2 ID="GRAPHMENU-USAGE-PLOTS">
    <TITLE>Add Usage Plots ...</TITLE>
    <PARA>
This menu item prompts the user for the name of a file which should contain
codon usage data in the same format as the data at <ULINK
URL="http://www.kazusa.or.jp/codon/" TYPE="external">this web
site</ULINK>.  If &prog; successfully loads the codon usage file two new
plots will be added to the display menu and will be immediately visible.  One
plot shows the codon scores (in a sliding window) for each of the forward
reading frames and the other shows the same thing for the reverse reading
frames. [short name: <LITERAL>codon_usage</LITERAL>]
    </PARA>

    <PARA>
The graph is calculated using the codon preference statistic
from <ULINK
URL="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=6694906&amp;dopt=Abstract">Gribskov
et al. (Nucl. Acids Res. 12; 539-549 (1984))</ULINK>.
    </PARA>

    <PARA>
Here is an example usage file:
      <SYNOPSIS>
UUU 32.2( 48423)  UCU 30.5( 45913)  UAU 21.8( 32829)  UGU  8.9( 13371)
UUC 13.0( 19519)  UCC 12.1( 18149)  UAC 11.8( 17721)  UGC  5.6(  8372)
UUA 26.0( 39138)  UCA 17.9( 26850)  UAA  1.3(  1944)  UGA  0.5(   733)
UUG 24.0( 36134)  UCG  8.0( 12055)  UAG  0.5(   705)  UGG 10.9( 16364)

CUU 25.3( 38015)  CCU 21.9( 32964)  CAU 16.3( 24577)  CGU 16.3( 24495)
CUC  7.3( 10922)  CCC  8.4( 12619)  CAC  6.4(  9653)  CGC  6.2(  9316)
CUA  8.6( 12957)  CCA 12.7( 19075)  CAA 27.3( 41066)  CGA  7.9( 11896)
CUG  6.3(  9503)  CCG  4.6(  6910)  CAG 10.9( 16457)  CGG  3.0(  4487)

AUU 35.0( 52636)  ACU 22.9( 34419)  AAU 33.9( 51009)  AGU 14.7( 22108)
AUC 12.6( 19000)  ACC 10.9( 16378)  AAC 17.9( 26895)  AGC  9.2( 13905)
AUA 13.1( 19726)  ACA 13.9( 20898)  AAA 39.3( 59079)  AGA 11.1( 16742)
AUG 20.9( 31376)  ACG  6.5(  9744)  AAG 25.2( 37825)  AGG  5.1(  7615)

GUU 29.3( 44015)  GCU 30.2( 45397)  GAU 38.1( 57240)  GGU 22.0( 33101)
GUC 11.0( 16497)  GCC 11.6( 17518)  GAC 15.8( 23749)  GGC  8.5( 12717)
GUA 12.3( 18451)  GCA 15.7( 23649)  GAA 44.3( 66550)  GGA 15.7( 23623)
GUG  8.3( 12422)  GCG  5.3(  8011)  GAG 21.3( 31979)  GGG  4.3(  6497)
      </SYNOPSIS>
    </PARA>
  </SECT2>

  <SECT2 ID="GRAPHMENU-ADD-USER-PLOT">
    <TITLE>Add User Plot ...</TITLE>
    <PARA>
&prog; is able to display some types of user data in a graph that looks like
the GC content graph (see <XREF LINKEND="GRAPHMENU-GC-CONTENT">).  This menu
item will prompt the user for the name of a data file which should contain one
of the following possible graph file formats:

</PARA>
   <ORDEREDLIST ID="GRAPH-FORMAT">
      <LISTITEM ID="GRAPH-FORMAT-1">
      <PARA>
       one line per base and one or more columns of integer or floating point 
       values per line. The number of lines should match the number of bases in
       the sequence. &prog; will plot each data point for the corresponding base.
       Each column represents a data set for a line. Example extract:

<SYNOPSIS>
21.4    1910.7
44      1126.1
1911.7  0
0       0
0       1782.0
1937.5  65.4
...
</SYNOPSIS>

      </PARA>
      </LISTITEM>
      <LISTITEM ID="GRAPH-FORMAT-2">
      <PARA>
      the first column corresponds to the base position and is an integer. 
      Note to distinguish this format from the previous format the first 
      line of the file must start with a '#'. Line colours can be specified
      in the header using the keyword colour followed by space separated
      R:G:B values for each line. The next rows(s) are the data 
      values. Example extract:

<SYNOPSIS>
# BASE  VAL1  VAL2  VAL3  VAL4  VAL5  VAL6
# colour 5:150:55 255:0:0 0:255:0 0:0:255 100:100:100 50:150:50
176 2204.8  848.23  0       0       0       536.04
278 804.99      0       837.2   0       681.63  0
452 0   699.98  0       0       0       251.18
553 0   0       0       0       0       52.4
654 0   0       0       0       334.2   0
686 0   0       652.78  0       0       0
831 0   0       0       0       0       67.97
...
</SYNOPSIS>

      </PARA>
      </LISTITEM>

      <LISTITEM ID="GRAPH-FORMAT-3">
      <PARA>
      indexed tab delimited file. For this tabix is used (see the 
      <ULINK URL="http://samtools.sourceforge.net/tabix.shtml">tabix manual</ULINK>)
      to create an index. This is especially useful for large data sets as it is memory 
      efficient and only reads the data corresponding to the visible region in &prog;.
      The first columns contain the sequence name and base position and this is then followed by
      the values to be plotted. 
      </PARA>
      <PARA>
      For example 'file.plot' is a tab delimited file with column 1 containing the sequence 
      name and column 2 the positions, this is sorted and then indexed with tabix:

<SYNOPSIS>
(grep ^"#" file.plot; grep -v ^"#" file.plot | sort -k1,1 -k2,2n) | bgzip > sorted.plot.gz ;
tabix -s 1 -b 2 -e 2 sorted.plot.gz
</SYNOPSIS>

Example extract:
<SYNOPSIS>
foo	1	5	5	129	5       5       239
foo	2	1	10	124	12      10      234
foo	3	5	16	129	12      15      229
foo	4	0	23	124	20      20      414
foo	5	5	22	121	28      25      419
foo	6	30	36	124	32      30      412
...
</SYNOPSIS>
      </PARA>
      </LISTITEM>

      <LISTITEM ID="GRAPH-FORMAT-4">
      <PARA>
      the next two formats are types of <ULINK
      URL="https://cgwb.nci.nih.gov/goldenPath/help/wiggle.html" TYPE="external">
      Wiggle formats</ULINK>. The first is variableStep. Note that &prog; only supports 
      the colour element in the track line.
      </PARA>
<SYNOPSIS>
track type=wiggle_0 color=255,200,0
variableStep chrom=chr19 span=10
310 1 
320 12 
330 18 
340 6 
350 5 
430 3 
440 1 
</SYNOPSIS>
      <PARA>
      Right clicking on the graph and selecting the
      'Configure...' option will display the 'Plot style' option for wiggle plots.
      The plots can be displayed as histograms or as a heat map.
      </PARA>
      </LISTITEM>
      <LISTITEM ID="GRAPH-FORMAT-5">
      <PARA>
      the next format supported by &prog; is fixedStep and is again a Wiggle format. 
      </PARA>
<SYNOPSIS>
track type=wiggle_0 name="fixedStep" description="fixedStep format" visibility=full autoScale=off viewLimits=0:1000 color=0,200,100 maxHeightPixels=100:50:20 graphType=points priority=20
fixedStep chrom=chr19 start=7401 step=300 span=200
1000
 900
 800
 700
 600
 500
 400
 300
 200
 100
</SYNOPSIS>
      </LISTITEM>
      <LISTITEM ID="GRAPH-FORMAT-6">
      <PARA>
      Blast tabular format. The blastall command must be run with the -m 8 flag which 
      generates one line of information per HSP. Alternatively the MSPcrunch file format
      can be read in as a graph file format. &prog; will prompt the user to determine
      whether it uses the query or subject coordinates to plot the graph.
      </PARA>
<SYNOPSIS>
</SYNOPSIS>
      </LISTITEM>

    </ORDEREDLIST>

<PARA>
When a file is prompted for there is an option which if selected will mean
the log transform is plotted.
</PARA>

  </SECT2>

  <SECT2 ID="GRAPHMENU-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="GRAPHMENU-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="GRAPHMENU-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="GRAPHMENU-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>.
    </PARA>
    <PARA>
See <ULINK
URL="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=10339816&amp;form=6&amp;db=m&amp;Dopt=b">Ishikawa,
J. and Hotta, K. FEMS Microbiol. Lett. 174:251-253 (1999)</ULINK> and <ULINK
URL="http://www.sanger.ac.uk/Software/Artemis/gc_plot/GC_frame.html">GC frame plot</ULINK> for more
information on the algorithm.
    </PARA>
    <PARA>
[Default: off] [short name: <LITERAL>gc_frame</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="GRAPHMENU-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="GRAPHMENU-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="GRAPHMENU-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.
    </PARA>
    <PARA>
See "Asymmetric substitution patterns in the two DNA strands of bacteria"
Lobry JR. - <ULINK
URL="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=8676740&amp;dopt=Abstract">Mol
Biol Evol 1996 May;13(5):660-5</ULINK>.
    </PARA>
    <PARA>
[Default: off] [short name: <LITERAL>gc_deviation</LITERAL>]
    </PARA>
  </SECT2>

  <SECT2 ID="GRAPHMENU-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="GRAPHMENU-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>.
    </PARA>
    <PARA>
[Default: off] [short name: <LITERAL>karlin_sig</LITERAL>]
    </PARA>
  </SECT2>


  <SECT2 ID="DISPLAYMENU-CUMULATIVEAT">
    <TITLE>Cumulative AT Skew and Cumulative GC Skew</TITLE>
    <PARA>
       AT skew is calculated as ([A]-[T])/([A]+[T]), where [A] and [T] are the counts of
       these bases in the window. 
       Grigoriev A (1999) <ULINK
URL="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=10225270"> 
Strand-specific compositional asymmetries in double-stranded DNA viruses. Virus Research 60, 1-19</ULINK>.
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-POSITIONALASYM">
    <TITLE>Positional Asymmetry</TITLE>
    <PARA>
       Shulman MJ, Steinberg CM, Westmoreland N (1981) <ULINK
URL="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=6456380"> 
The coding function of nucleotide sequences can be discerned by statistical analysis. J Theor Biol
88:409-20</ULINK>.
    </PARA>
  </SECT2>

   <SECT2 ID="DISPLAYMENU-ENTROPY">
    <TITLE>Informational Entropy</TITLE>
    <PARA>
       Konopka Andrzej (1984) <ULINK
URL="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=6738090"> 
Is the information content of DNA evolutionarily significant? J Theor Biol 107:697-704</ULINK>.

Informational entropy is calculated from a table of overlapping DNA 
triplet frequencies, using equation 1 in the above reference. 
The use of overlapping triplets smooths the frame effect.
    </PARA>
  </SECT2>
 
  <SECT2 ID="DISPLAYMENU-SCALEDCHISQ">
    <TITLE>Scaled Chi Square</TITLE>
    <PARA>
      Shields DC, Sharp PM (1987) <ULINK 
URL="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=3118331">
Synonymous codon usage in Bacillus subtilis 
reflects both translational selection and mutational biases. Nucleic Acids 
Res 15:8023-40</ULINK>.
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-MUTRES">
    <TITLE>Mutational Response Index</TITLE>
    <PARA>
      Gatherer D, McEwan NR (1997) <ULINK
URL="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=9315288">
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</ULINK>.
    </PARA>
  </SECT2>

  <SECT2 ID="DISPLAYMENU-NC">
    <TITLE>Effective Codon Number</TITLE>
    <PARA>
      Wright F (1990) <ULINK
URL="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=2110097">
The 'effective number of codons' used in a gene. Gene 87:23-9</ULINK>, and Fuglsang A (2004) <ULINK
URL="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=15081433">
The 'effective number of codons' revisited. Biochem Biophys Res Commun. May 7;317(3):957-64</ULINK>. 
    </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) <ULINK
URL="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=pubmed&amp;dopt=Abstract&amp;list_uids=8112587">
Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes. Gene 139:43-9</ULINK>.
    </PARA>
  </SECT2>

</SECT1>