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<SECT1 ID="ENTRIESMENU">
<TITLE>The Entries Menu</TITLE>
<PARA>
The items in this menu are used to change which entry is the default entry and
which entries are active (see <XREF LINKEND="CONCEPTS-ENTRY">). At the
bottom of the menu there is a toggle button for each entry which controls
whether the entry is active or not.<![ %artemis-only; [ These toggle buttons
work in a similar way the the buttons on the entry button line (see <XREF
LINKEND="ENTRYBUTTONS">).]]>
</PARA>
<PARA>
Here is a description of the other menu items:
</PARA>
<SECT2 ID="ENTRIESMENU-SET-NAME-OF-ENTRY">
<TITLE>Set Name Of Entry</TITLE>
<PARA>
Set the name of an entry chosen from a sub-menu. The name of the entry is
used as the name of the file when the entry is saved.
</PARA>
</SECT2>
<SECT2 ID="ENTRIESMENU-SET-DEFAULT-ENTRY">
<TITLE>Set Default Entry</TITLE>
<PARA>
Set the default entry by choosing one of the entries from the sub-menu. (See
<XREF LINKEND="CONCEPTS-DEFAULTENTRY">).
</PARA>
</SECT2>
<SECT2 ID="ENTRIESMENU-REMOVE-AN-ENTRY">
<TITLE>Remove An Entry</TITLE>
<PARA>
Remove an entry from &prog; by choosing one of the entries from the sub-menu.
The original file that this entry came from (if any) will not be removed.
</PARA>
</SECT2>
<SECT2 ID="ENTRIESMENU-REMOVE-ACTIVE-ENTRIES">
<TITLE>Remove Active Entries</TITLE>
<PARA>
Remove the entries that are currently active. (See <XREF
LINKEND="CONCEPTS-ACTIVEENTRY">).
</PARA>
</SECT2>
<SECT2 ID="ENTRIESMENU-DEACTIVATE-ALL">
<TITLE>Deactivate All Entries</TITLE>
<PARA>
Choosing this menu item will deactivate all entries. (See <XREF
LINKEND="CONCEPTS-ACTIVEENTRY">.)
</PARA>
</SECT2>
</SECT1>
<SECT1 ID="SELECTMENU">
<TITLE>The Select Menu</TITLE>
<PARA>
The items in this menu are used to modify the current selection (see <XREF
LINKEND="CONCEPTS-SELECTION">). &art;<![ %artemis-only; [ shows a short summary of
the current selection at the top of the main window (see <XREF
LINKEND="MAINWINDOW-BREAKDOWN-SELECTIONSTATUS"> for details).]]>.
</PARA>
<SECT2 ID="SELECTMENU-FEATURE-SELECTOR">
<TITLE>Feature Selector ...</TITLE>
<PARA>
Open a new Feature Selector window. This window allows the user to choose
which features to select or view based on feature keys (see <XREF
LINKEND="CONCEPTS-KEY">), qualifier values (see <XREFLINKEND="CONCEPTS-QUALIFIERS">) and amino acid motifs.
</PARA>
<PARA>
The Select button will set the selection to the contain those features that
match the given key, qualifier and amino acid motif combination.
</PARA>
<PARA>
The View button will create a new feature list (see <XREF
LINKEND="FEATURELIST">) containing only those features that
match the given key, qualifier and amino acid motif combination.
</PARA>
<SCREENSHOT>
<SCREENINFO>
The Selector window
</SCREENINFO>
<MEDIAOBJECT>
<IMAGEOBJECT>
<IMAGEDATA FORMAT="gif" FILEREF="selector.gif">
</IMAGEOBJECT>
<IMAGEOBJECT>
<IMAGEDATA FORMAT="eps" FILEREF="selector.eps">
</IMAGEOBJECT>
</MEDIAOBJECT>
</SCREENSHOT>
</SECT2>
<SECT2 ID="SELECTMENU-ALL">
<TITLE>All</TITLE>
<PARA>
Reset the selection so that nothing is selected then select all the features
in the active entries. [shortcut key: A]
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-ALLBASES">
<TITLE>All Bases</TITLE>
<PARA>
Reset the selection so that nothing is selected then select all the bases in
the sequence.
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-ALLFEATURES-NONMATCHING-REGIONS">
<TITLE>Select All Features in Non-matching Regions</TITLE>
<PARA>
Select all features that have no corresponding match in ACT. This is used to
higlight regions that are different between sets of sequence. It will only take
into account matches that have not been filtered out using the score, identity
or length cut-off.
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-NONE">
<TITLE>None</TITLE>
<PARA>
Clear the selection so that nothing is selected. [shortcut key: N]
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-BY-KEY">
<TITLE>By Key</TITLE>
<PARA>
Ask the user for a feature key, reset the selection so that nothing is
selected, then select all the features with the key given by the user.
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-CDS-FEATURES">
<TITLE>CDS Features</TITLE>
<PARA>Reset the selection so that nothing is selected, then select all the CDS
features that do not have a /pseudo qualifier.
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-SAME-KEY">
<TITLE>Same Key</TITLE>
<PARA>
Select all the features that have the same key as any of the currently
selected features.
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-ORF">
<TITLE>Open Reading Frame</TITLE>
<PARA>
Extend the current selection of bases to cover complete open reading frames.
Selecting a single base or codon and then choosing this menu item has a
similar effect to double clicking the middle button on a base or residue (see
<XREF LINKEND="VIEWS-SELECTION"> for details).
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-OVERLAPPING-SELECTION">
<TITLE>Features Overlapping Selection</TITLE>
<PARA>
Select those (and only those) features that overlap the currently selected
range of bases or any of the currently selected features. The current
selection will be discarded.
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-WITHIN-SELECTION">
<TITLE>Features Within Selection</TITLE>
<PARA>
Select those (and only those) features that are fully contained by the currently
selected range of bases or any of the currently selected features. The current
selection will be discarded.
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-BASE-RANGE">
<TITLE>Base Range ...</TITLE>
<PARA>
Ask the user for a range of bases, then select those bases. The range should
look something like this: <LITERAL>100-200</LITERAL>,
<LITERAL>complement(100..200)</LITERAL>, <LITERAL>100.200</LITERAL> or
<LITERAL>100..200</LITERAL>. If the first number is larger than the
second the bases will be selected on the forward strand, otherwise they will
be selected on the reverse strand (unless there is a
<LITERAL>complement</LITERAL> around the range, in which case the sense is
reversed).
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-FEATURE-AA-RANGE">
<TITLE>Feature AA Range ...</TITLE>
<PARA>
Ask the user for a range of amino acids in the selected feature and select
those bases. The range should look something like this:
<LITERAL>100-200</LITERAL>, or <LITERAL>100..200</LITERAL>.
</PARA>
</SECT2>
<SECT2 ID="SELECTMENU-TOGGLE-SELECTION">
<TITLE>Toggle Selection</TITLE>
<PARA>
Invert the selection - after choosing this menu item the selection willcontain only those features that were not in the selection beforehand.
</PARA>
</SECT2>
</SECT1>
<SECT1 ID="VIEWMENU">
<TITLE>The View Menu</TITLE>
<PARA>
</PARA>
<SECT2 ID="VIEWMENU-VIEW-SELECTED-FEATURES">
<TITLE>Selected Features</TITLE>
<PARA>
Open a view window for each selected feature showing it's feature table entry.
[shortcut key: V]
</PARA>
</SECT2>
<SECT2 ID="VIEWMENU-VIEW-SELECTION">
<TITLE>Selection</TITLE>
<PARA>
Open a view window that will show the current selection. The window is
updated as the selection changes, so it can be left open.
</PARA>
<PARA>
When one feature is selected the window will show the text (EMBL, GenBank or
GFF format) of the feature, the base composition, GC percentage, correlation
score (see <XREF LINKEND="GRAPHMENU-CORRELATION-SCORES">), and the bases and
translation of the sequence of the feature.
</PARA>
<PARA>
When two or more features are selected the window will show the text (EMBL,
GenBank or GFF format) of the features, the base composition, average GC
percentage, average correlation score, minimum/maximum GC content and
minimum/maximum correlation score of the feature sequence.
</PARA>
<PARA>
When a range of bases is selected the window will show the base composition,
GC content percentage and the bases and translation of the sequence of the
feature.
</PARA>
</SECT2>
<SECT2 ID="VIEWMENU-SEARCH-RESULTS">
<TITLE>Search Results</TITLE>
<PARA>
On this sub-menu allows the user to view the results of feature searches that
are launched from the run menu in &art;<![ %artemis-only; [ (see <XREF
LINKEND="RUNMENU">)]]>.
</PARA>
</SECT2>
<SECT2 ID="VIEWMENU-SHOW-CDS-GENES-PRODUCTS">
<TITLE>CDS Genes And Products</TITLE>
<PARA>
Pop up a feature list (see <XREF LINKEND="FEATURELIST">) of the CDS showing
the gene names (from the /gene qualifier) and
the product (from the /product qualifier). This list includes pseudo genes.
</PARA>
</SECT2>
<SECT2 ID="VIEWMENU-FEATURE-FILTERS">
<TITLE>Feature Filters</TITLE>
<PARA>
Each of the items in this sub-menu each allow the user to view a subset of the
active features. An example of a subset is all those features with
<LITERAL>misc_feature</LITERAL> as a key. The features are displayed in a new
window that contains a menu bar with possible actions to apply to the subset,
and feature list (see <XREF LINKEND="FEATURELIST">). Most of the possibleactions will apply only to the features in the list. For example "Show
Overview" in the View menu (see <XREF LINKEND="VIEWMENU-SHOW-OVERVIEW">) will
include statistics only on the features in the list.
</PARA>
<SECT3 ID="VIEWMENU-FEATURE-FILTERS-SUSPSTART">
<TITLE>Suspicious Start Codons ...</TITLE>
<PARA>
Show those CDS features that have a suspicious start codon. ie. the first
codon of the feature isn't ATG (in eukaroytic mode) or ATG, GTG and TTG (in
prokaryotic mode). This function is effected by the setting of the
"Eukaroytic Mode" option in the main options menu (see <XREF
LINKEND="LAUNCH-WINDOW-OPTIONS-EUK"> for more).
</PARA>
</SECT3>
<SECT3 ID="VIEWMENU-FEATURE-FILTERS-SUSPSTOP">
<TITLE>Suspicious Stop Codons ...</TITLE>
<PARA>
Show those CDS features that have a suspicious stop codon. ie. the last codon
of the feature isn't one of TAA, TAG or TGA.
</PARA>
</SECT3>
<SECT3 ID="VIEWMENU-FEATURE-FILTERS-NONEMBLKEYS">
<TITLE>Non EMBL Keys ...</TITLE>
<PARA>
Show those features that have a key that isn't valid for EMBL/GenBank
entries.
</PARA>
</SECT3>
<SECT3 ID="VIEWMENU-FEATURE-FILTERS-">
<TITLE>Duplicated Features ...</TITLE>
<PARA>
Show those features that are duplicated (ie. features that have the same key
and location as another feature). These sort of duplicates aren't allowed by
the EMBL database.
</PARA>
</SECT3>
<SECT3 ID="VIEWMENU-FEATURE-FILTERS-OVERLAPPING">
<TITLE>Overlapping CDS Features ...</TITLE>
<PARA>
Show those CDS features that overlap another CDS feature (on either strand).
</PARA>
</SECT3>
<SECT3 ID="VIEWMENU-FEATURE-FILTERS-REQQUAL">
<TITLE>Features Missing Required Qualifiers ...</TITLE>
<PARA>
Show those features that are missing a qualifier that is required by the EMBL
database.
</PARA>
</SECT3>
<SECT3 ID="VIEWMENU-FEATURE-FILTERS-BYKEY">
<TITLE>Filter By Key ...</TITLE>
<PARA>
Show those features that have a key chosen by the user.
</PARA>
</SECT3>
<SECT3 ID="VIEWMENU-FEATURE-FILTERS-SELECTED">
<TITLE>Selected Features ...</TITLE>
<PARA>
Show the currently selected features in a new feature list. The contents of
the list will remain the same even if selection subsequently changes. This is
useful for bookmarking a collection of features for later use.
</PARA> </SECT3>
</SECT2>
<SECT2 ID="VIEWMENU-SHOW-OVERVIEW">
<TITLE>Overview</TITLE>
<PARA>
Open a new window the will show a summary of the active entries and some
statistics about the sequence (such as the GC content).
[shortcut key: O]
</PARA>
<SECT3 ID="VIEWMENU-SHOW-OVERVIEW-SEQSTATS">
<TITLE>Sequence Statistics</TITLE>
<PARA>
The overview window show the following statistics about the sequence:
<ITEMIZEDLIST>
<LISTITEM>
<PARA>
Number of bases.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
GC percentage.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
The number of each nucleotide in the sequence.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
GC percentage of non-ambiguous bases - ie. the GC content percentage ignoring
bases other than A,T,C and G. This should be the same as the "GC percentage"
above.
</PARA>
</LISTITEM>
</ITEMIZEDLIST>
</PARA>
</SECT3>
<SECT3 ID="VIEWMENU-SHOW-OVERVIEW-FEATURESTATS">
<TITLE>Feature Statistics</TITLE>
<PARA>
The overview window also shows the following statistics about the features in
the active entries (if there are any features). Note that the "genes" are the
non-pseudo CDS features.
<ITEMIZEDLIST>
<LISTITEM>
<PARA>
Number of features in the active entries (see <XREF
LINKEND="CONCEPTS-ACTIVEENTRY">).
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
Gene density - the average number of non-pseudo CDS features per 1000 bases.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
Average gene length - the average length of non-pseudo CDS features (not
including introns).
</PARA> </LISTITEM>
<LISTITEM>
<PARA>
Number of non-spliced genes.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
Number of spliced genes.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
Number of pseudo genes (ie. CDS features with a /pseudo qualifier).
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
Protein coding (CDS) features.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
Protein coding (CDS) bases.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
Protein coding percentage - ie. the number of coding bases excluding introns.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
Coding percentage (including introns).
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
A summary of the number of features of each key (type) and their colours.
</PARA>
</LISTITEM>
</ITEMIZEDLIST>
</PARA>
</SECT3>
</SECT2>
<SECT2 ID="VIEWMENU-SHOW-FORWARD-OVERVIEW">
<TITLE>Forward Strand Overview</TITLE>
<PARA>
Open a new window the will show a summary of the features and bases of the
forward strand.
</PARA>
</SECT2>
<SECT2 ID="VIEWMENU-SHOW-REVERSE-OVERVIEW">
<TITLE>Reverse Strand Overview</TITLE>
<PARA>
Open a new window the will show a summary of the features and bases of the
reverse strand.
</PARA>
</SECT2>
<SECT2 ID="VIEWMENU-VIEW-FEATURE-BASES">
<TITLE>Feature Bases</TITLE>
<PARA>
Create a view window for each selected feature, which shows bases of the
feature.
</PARA>
</SECT2>
<SECT2 ID="VIEWMENU-VIEW-FEATURE-BASES-FASTA">
<TITLE>Feature Bases As FASTA</TITLE>
<PARA>
Create a view window for each selected feature, which shows bases of the
feature in FASTA format.
</PARA>
</SECT2>
<SECT2 ID="VIEWMENU-VIEW-FEATURE-AMINO-ACIDS">
<TITLE>Feature Amino Acids</TITLE>
<PARA>
Create a view window for each selected feature, which shows amino acids of the
feature.
</PARA>
</SECT2>
<SECT2 ID="VIEWMENU-VIEW-FEATURE-AMINO-ACIDS-FASTA">
<TITLE>Feature Amino Acids As FASTA</TITLE>
<PARA>
Create a view window for each selected feature, which shows amino acids of the
feature in FASTA format.
</PARA>
</SECT2>
<SECT2 ID="VIEWMENU-SHOW-FEATURE-STATISTICS">
<TITLE>Feature Statistics</TITLE>
<PARA>
Show some statistics about each selected feature. On the left on the feature
information window is the amino acid composition of the feature. On the right
is the codon composition of the feature.
</PARA>
</SECT2>
<SECT2 ID="VIEWMENU-SHOW-FEATURE-PLOTS">
<TITLE>Feature Plots</TITLE>
<PARA>
Open a window for each selected feature that shows a plot of the
Kyte-Doolittle Hydrophobicity [short name: <LITERAL>hydrophobicity</LITERAL>],
the Hopp-Woods Hydrophilicity [short name: <LITERAL>hydrophilicity</LITERAL>],
and an approximation of the GCG Coiled Coils algorithm [short name:
<LITERAL>coiled_coil</LITERAL>]. (For more detail about the coiled coils
algorithm see "Predicting Coiled Coils from Protein Sequences", Science
Vol. 252 page 1162.) [shortcut key: W]
</PARA>
<PARA>
Some general information about graphs and plots in &prog; can be found in <XREF
LINKEND="GRAPHS">. Configuration options for graphs are described in <XREF
LINKEND="OPTIONS-PLOTS">.
</PARA>
</SECT2>
</SECT1>
<SECT1 ID="GOTOMENU">
<TITLE>The Goto Menu</TITLE>
<PARA>
The items in this menu allow the user to navigate around the sequence and
features.
</PARA>
<SECT2 ID="GOTOMENU-NAVIGATOR">
<TITLE>Navigator ...</TITLE>
<PARA>Open a new navigation window. [shortcut key: G]
</PARA>
<PARA>
This window allows the user to perform five
different tasks:
<ORDEREDLIST>
<LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-BASE">
<FORMALPARA>
<TITLE>
Scroll all the views so that a particular base is in the centre of
the display
</TITLE>
<PARA>
To use this function, type a base position into the
box to the right of the "Goto Base:" label then press the goto button at the
bottom of the window. The requested base will be selected and then the
overview display and the DNA display will scroll so that the base is as near
as possible to the middle of the main window.
</PARA>
</FORMALPARA>
</LISTITEM>
<LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-GENENAME">
<FORMALPARA>
<TITLE>
Find the next feature that has the given gene name
</TITLE>
<PARA>
To use this function, type a gene name into the box to the right of the "Goto
Feature With This Gene Name:" label and then press the goto button.
&prog; will select the first feature with the given text in any of it's
qualifiers and will then scroll the display so that feature is in view.
</PARA>
</FORMALPARA>
</LISTITEM>
<LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-TEXT">
<FORMALPARA>
<TITLE>
Find the next feature that has a qualifier containing a particular string
</TITLE>
<PARA>
To use this function, type a string into the box to the right of the "Goto
Feature With This Qualifier Value:" label and then press the goto button.
&prog; will select the first feature with the given string in any of it's
qualifier values (see <XREF LINKEND="CONCEPTS-QUALIFIERS">) and will then
scroll the display so that feature is in view.
</PARA>
</FORMALPARA>
</LISTITEM>
<LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-KEY">
<FORMALPARA>
<TITLE>
Find the next feature that has a particular key
</TITLE>
<PARA>
To use this function, type a key into the box to the right of the "Goto
Feature With This Key:" label and then press the goto button. &prog; will
select the first feature with the given key and will then scroll the display
so that feature is in view.
</PARA>
</FORMALPARA>
</LISTITEM>
<LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-DNA-PATTERN">
<FORMALPARA>
<TITLE>
Find the next occurrence of a particular base pattern in the sequence
</TITLE>
<PARA>
To use this function, type a base pattern into the box to the right of the
"Find Base Pattern:" label and then press the goto button. &prog; will select
the first contiguous group of bases on either strand that match the given basepattern and will then scroll the display so that those bases are in view.
Any IUB base code can be used in the pattern, so for example searching for
<LITERAL>aanntt</LITERAL> will match any six bases that start with "aa" and
ends with "tt". See <XREF LINKEND="IUB-BASE-CODES"> for a list of the
available base codes.
</PARA>
</FORMALPARA>
</LISTITEM>
<LISTITEM ID="GOTOMENU-NAVIGATOR-GOTO-AA-PATTERN">
<FORMALPARA>
<TITLE>
Find the next occurrence of a particular residue pattern in the sequence
</TITLE>
<PARA>
To use this function, type a amino acid pattern into the
box to the right of the "Goto Amino Acid String:" label and then press the
goto button. &prog; will select the first contiguous group of bases on either
strand that translate to the given amino acids and will then scroll the
display so that those bases are in view. The letter 'X' can be used as an
ambiguity code, hence 'AAXXXDD' will match 'AALRTDD' or 'AATTTDD' etc.
</PARA>
</FORMALPARA>
</LISTITEM>
</ORDEREDLIST>
</PARA>
<PARA>
Note that for all the functions above except the first ("Goto Base"), if the
"Start search at beginning" option is set or if there is nothing selected the
search will start at the beginning of the sequence. Otherwise the search will
start at the selected base or feature. This means that the user can step
through the matching bases or features by pressing the goto button repeatedly.
</PARA>
<PARA>
If the "Ignore Case" toggle is on (which is the default) Artemis will
ignore the difference between upper and lower case letters when searching for
a gene name, a qualifier value or a feature key.
</PARA>
<PARA>
The "Allow Substring Matches" toggle affects <XREF
LINKEND="GOTOMENU-NAVIGATOR-GOTO-GENENAME"> and <XREF
LINKEND="GOTOMENU-NAVIGATOR-GOTO-TEXT">. If on &prog; will search for
qualifier values that contain the given characters. For example searching for
the genename CDC will find CDC1, CDC2, ABCDC etc. If the toggle is off &prog;
will only find exact matches, so searching for the gene CDC will only find
features that have <LITERAL>/gene="CDC"</LITERAL> not
<LITERAL>/gene="CDC11"</LITERAL>.
</PARA>
</SECT2>
<SECT2 ID="GOTOMENU-GOTO-SELECTION-START">
<TITLE>Start of Selection</TITLE>
<PARA>
Scroll all the views so that the first base of the selection is as close to
the centre as possible. If the a range of bases is selected the views will
move to the first base of the range. If one or more features are selected,
then the first base of the first selected feature will be centred. Otherwise,
if one or more segments (see <XREF LINKEND="CONCEPTS-SEGMENT">) is selected
then the first base of the first selected segment will be centred.
[shortcut key: control-left]
</PARA>
</SECT2>
<SECT2 ID="GOTOMENU-GOTO-SELECTION-END">
<TITLE>End of Selection</TITLE>
<PARA>
This does the same as "Goto Start of Selection", but uses the last base of the
selected range or the last base of the last selected feature or segment.
[shortcut key: control-right]
</PARA>
</SECT2>
<SECT2 ID="GOTOMENU-GOTO-FEATURE-START">
<TITLE>Feature Start</TITLE>
<PARA>
Scroll the views to the start of the first selected feature.
</PARA>
</SECT2>
<SECT2 ID="GOTOMENU-GOTO-FEATURE-END">
<TITLE>Feature End</TITLE>
<PARA>
Scroll the views to the end of the first selected feature.
</PARA>
</SECT2>
<SECT2 ID="GOTOMENU-GOTO-START-OF-SEQ">
<TITLE>Start of Sequence</TITLE>
<PARA>
Scroll the views so that the start of the sequence is visible.
[shortcut key: control-up]
</PARA>
</SECT2>
<SECT2 ID="GOTOMENU-GOTO-END-OF-SEQ">
<TITLE>End of Sequence</TITLE>
<PARA>
Scroll the views so that the end of the sequence is visible.
[shortcut key: control-down]
</PARA>
</SECT2>
<SECT2 ID="GOTOMENU-GOTO-FEATURE-BASE-POSITION">
<TITLE>Feature Base Position ...</TITLE>
<PARA>
Ask the user for a base position within the first selected feature, then
scroll the views so that that base position is centred.
</PARA>
</SECT2>
<SECT2 ID="GOTOMENU-GOTO-FEATURE-AMINO-ACID">
<TITLE>Feature Amino Acid ...</TITLE>
<PARA>
Ask the user for an amino acid position within the first selected feature,
then scroll the views so that that position is centred.
</PARA>
</SECT2>
</SECT1>
<SECT1 ID="EDITMENU">
<TITLE>The Edit Menu</TITLE>
<PARA>
This menu contains most of the functions that change the entries. Note that
the changes will not be saved back to the original files until one of the save
functions in the File menu is used<![ %artemis-only; [
(see <XREF LINKEND="FILEMENU-SAVE-AN-ENTRY">)]]>.
</PARA>
<SECT2 ID="EDITMENU-UNDO">
<TITLE>Undo</TITLE>
<PARA>
This function will undo the last change that was made using the Edit or Create
menus. Up to 20 changes can be undone. This menu item is only enabled when
there is something to undo. This limit can be changed in the
options file (see <XREF LINKEND="OPTIONS-UNDO-LEVELS">). [shortcut key: U]
</PARA>
</SECT2>
<SECT2 ID="EDITMENU-REDO">
<TITLE>Redo</TITLE>
<PARA>This function will redo the last undo operation.
</PARA>
</SECT2>
<SECT2 ID="EDITMENU-EDIT-SELECTED-FEATURES">
<TITLE>Selected Features in Editor</TITLE>
<PARA>
Open an edit window for each selected feature. [shortcut key: E]
</PARA>
<SCREENSHOT>
<SCREENINFO>
The feature edit window
</SCREENINFO>
<MEDIAOBJECT>
<IMAGEOBJECT>
<IMAGEDATA FORMAT="gif" FILEREF="feature_edit.gif">
</IMAGEOBJECT>
</MEDIAOBJECT>
</SCREENSHOT>
<PARA>
From the top down the edit window has these parts:
<ORDEREDLIST>
<LISTITEM>
<PARA>
At the top left is a selector for choosing the key of the feature. This
only contains a subset of the legal keys. The subset can be changed by
changing the <LITERAL>common_keys</LITERAL> option in the options file (see
<XREF LINKEND="OPTIONS-COMMONKEYS">).
</PARA>
<PARA>
At the top right of the edit window is a selector for adding a qualifier. For
example choosing <LITERAL>note</LITERAL> from the menu will insert
<LITERAL>/note=""</LITERAL> into the qualifier edit area.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
Just below the key and qualifier selector is the location entry field. &prog;
understands most of the EMBL location syntax, including joins, complements,
ranges with non-exact ends (eg. <LITERAL>(100.200)..>350</LITERAL>) and
references to other entries
(eg. <LITERAL>join(100..200,SPB23A1:100..200)</LITERAL>).
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
Below the location is a row of buttons:
</PARA>
<ITEMIZEDLIST>
<LISTITEM>
<PARA>
The <LITERAL>Complement</LITERAL> button will complement the contents of the
location field.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
The <LITERAL>Grab Range</LITERAL> button will grab the currently selected
range into the location field.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
The <LITERAL>Remove Range</LITERAL> button will remove the selected bases from
the location string. This is normally used to create an intron in a feature.
</PARA>
</LISTITEM> <LISTITEM>
<PARA>
Pressing the <LITERAL>Goto Feature</LITERAL> button has the same effect as the
"Start of Selection" item in the "Goto" menu. (See <XREF
LINKEND="GOTOMENU-GOTO-SELECTION-START"> for more).
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
The <LITERAL>User Qualifiers</LITERAL> button opens a tool for maintaining
user defined lists of qualifiers (i.e. qualifiers in the form tag = value pairs
on separate lines) and the option to read qualifiers from <ULINK
URL="http://www.geneontology.org/GO.format.shtml" TYPE="external">OBO</ULINK> formatted files or
URLs. In the intial screen (see below) you are invited to import your qualifier list from the import
options in the "File" menu. These lists can be optionally saved between sessions in the file
'.artemis.qualifiers' in the home directory.
</PARA>
<MEDIAOBJECT>
<IMAGEOBJECT>
<IMAGEDATA FORMAT="gif" FILEREF="qualifier_list.gif">
</IMAGEOBJECT>
</MEDIAOBJECT>
<PARA>
When a qualifier list or OBO file has been added then it is possible to search for
keywords within a list. The qualifer selected in the drop down list (under the SEARCH button)
can then be added to the current feature annotation or added to selected features in &prog;.
If the keywords text field is left blank then all qualifiers are available from the drop
down list of qualifier values.
</PARA>
<MEDIAOBJECT>
<IMAGEOBJECT>
<IMAGEDATA FORMAT="gif" FILEREF="qualifier_list2.gif">
</IMAGEOBJECT>
</MEDIAOBJECT>
</LISTITEM>
</ITEMIZEDLIST>
</LISTITEM>
<LISTITEM>
<PARA>
The centre of the edit window contains the qualifier entry section. The
qualifiers should be entered the in same way the appear in the feature table
part of an EMBL entry, but without the leading <LITERAL>FT</LITERAL> and
spaces.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
The bottom of the window contains three buttons. The <LITERAL>OK</LITERAL>
button will update the feature with the changes that have been made by the
user and will then close the edit window. The <LITERAL>Cancel</LITERAL>
button will discard the changes and then close the window. The
<LITERAL>Apply</LITERAL> will make the changes, but will not close the
window. Before any changes are made the location and the qualifiers are
checked for formatting errors. Any errors will brought to the attention of
the user through the use of annoying pop-up boxes. No changes will be
performed until there all errors have been fixed.
</PARA>
</LISTITEM>
</ORDEREDLIST>
</PARA>
</SECT2>
<SECT2 ID="EDITMENU-SUBSEQUENCE">
<TITLE>Subsequence (and Features)</TITLE> <PARA>
Make a copy (in a new edit window) of the selected bases and the features in
that range. Any features that overlap the end of the range will be truncated.
</PARA>
</SECT2>
<SECT2 ID="EDITMENU-FINDANDREPLACE">
<TITLE>Find Or Replace Qualifier Text</TITLE>
<PARA>
This opens a search window with options to find or replace qualifier
text. The search can be restricted to features with a given key and/or
it can be restricted to a given qualifier name.
</PARA>
<PARA>
Boolean operators (and/or) can be used in the search. Clicking on the
<LITERAL>Show Boolean Search Options</LITERAL> displays 4 options.
<ORDEREDLIST>
<LISTITEM>
<PARA>
The <LITERAL>Use boolean operators (and, or, & |)</LITERAL> means that
it uses any of these operators that are in the <LITERAL>Find</LITERAL> text field.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
The <LITERAL>Match any string (i.e. x OR y)</LITERAL> means that the words in
the <LITERAL>Find</LITERAL> text field will be separated by an OR
condition. So that it finds those features with qulaifiers that contain any of the
words.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
The <LITERAL>Match all string (i.e. x AND y)</LITERAL> means that the words in
the <LITERAL>Find</LITERAL> text field will be separated by an AND
condition. So that it finds those features with qulaifiers that contain all of the
words.
</PARA>
</LISTITEM>
<LISTITEM>
<PARA>
The <LITERAL>No boolean search</LITERAL> option is the default. This
means it searches for those features with qualifiers that contain the complete
text from the <LITERAL>Find</LITERAL> text field.
</PARA>
</LISTITEM>
</ORDEREDLIST>
</PARA>
<PARA>
In addition selecting the Duplicate Qualifiers tab provides options to
search for or delete duplicate qualifiers.
</PARA>
</SECT2>
<SECT2 ID="QUALIFIERS">
<TITLE>Qualifier(s) of Selected Feature</TITLE>
<SECT3 ID="EDITMENU-CHANGE-QUALIFIERS">
<TITLE>Change ...</TITLE>
<PARA>
This function allows the user to add or change qualifiers on all the selected
features in one operation. The main part of the window acts like the
qualifier editing field of the feature edit window (see <XREF
LINKEND="EDITMENU-EDIT-SELECTED-FEATURES">).
</PARA>
</SECT3>
<SECT3 ID="EDITMENU-REMOVE-QUALIFIERS">
<TITLE>Remove ...</TITLE> <PARA>
This function allows the user to remove all qualifiers with a particular name
from all the selected features.
</PARA>
</SECT3>
<SECT3 ID="EDITMENU-CONVERT-QUALIFIERS">
<TITLE>Convert ...</TITLE>
<PARA>
This function allows the user to convert all qualifiers of a particular type
to another qualifier for all the selected features.
</PARA>
</SECT3>
</SECT2>
<SECT2 ID="EDITMENU-SELECTED-FEATURES">
<TITLE>Selected Feature(s)</TITLE>
<SECT3 ID="EDITMENU-DUPLICATE-SELECTED-FEATURES">
<TITLE>Duplicate</TITLE>
<PARA>
Make a copy of each selected feature. Each new feature will be added just
after the original in the same entry as the original. [shortcut key: D]
</PARA>
</SECT3>
<SECT3 ID="EDITMENU-MERGE-SELECTED-FEATURES">
<TITLE>Merge</TITLE>
<PARA>
Create a new feature that contains all the exons and qualifiers of the
selected features. The selected features must all have the same key.
[shortcut key: M]
</PARA>
</SECT3>
<SECT3 ID="EDITMENU-UNMERGE-SELECTED-FEATURE">
<TITLE>Unmerge</TITLE>
<PARA>
If the selection contains exactly two exons and those exons are adjacent in
the same feature, split the feature into two pieces between the exons. The
original feature is truncated and a new feature is created. The qualifiers of
the old feature are copied to new feature.
</PARA>
</SECT3>
<SECT3 ID="EDITMENU-UNMERGE-ALL-SEGMENTS">
<TITLE>Unmerge All Segments</TITLE>
<PARA>
All exons in a feature are unmerged.
</PARA>
</SECT3>
<SECT3 ID="EDITMENU-DELETE-SELECTED-FEATURES">
<TITLE>Delete</TITLE>
<PARA>
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. Thedefault 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: <pattern>",
where <pattern> 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>, <ULINK URL="http://pfam.sanger.ac.uk/"
TYPE="external">Pfam</ULINK> and <ULINK URL="http://rfam.sanger.ac.uk/"
TYPE="external">Rfam</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 forwardreading 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&db=PubMed&list_uids=6694906&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>
<![ %artemis-only; [
Indexed user plots can be used with indexed FASTA sequences and indexed GFF files (see
<XREF LINKEND="FILETYPES">). The sequence can then be changed using the drop down menu in
the Entry toolbar and this will change the graph data to the selected sequence.]]>
</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&form=6&db=m&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&db=PubMed&list_uids=8676740&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&db=PubMed&list_uids=10066522&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&db=pubmed&dopt=Abstract&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&db=pubmed&dopt=Abstract&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&db=pubmed&dopt=Abstract&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&db=pubmed&dopt=Abstract&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&db=pubmed&dopt=Abstract&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&db=pubmed&dopt=Abstract&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&db=pubmed&dopt=Abstract&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&db=pubmed&dopt=Abstract&list_uids=8112587">
Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes. Gene 139:43-9</ULINK>.
</PARA>
</SECT2>
</SECT1>