Alignment Annotation

From c73e1efb0b980e9faa642cbae090a58f952c33ac Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 21 Sep 2016 12:29:49 +0100 Subject: [PATCH] JAL-2189 reworked annotation docs JAL-2171 autocomplete RNA ss symbol for interactive annotation --- help/html/features/annotation.html | 334 +++++++++++++++++++++--------------- 1 file changed, 199 insertions(+), 135 deletions(-) diff --git a/help/html/features/annotation.html b/help/html/features/annotation.html index 7e52c46..d13afe4 100755 --- a/help/html/features/annotation.html +++ b/help/html/features/annotation.html @@ -19,142 +19,206 @@ * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Alignment Annotation + +Alignment Annotation + -

Alignment Annotation

+ Alignment Annotation +

In addition to the definition of groups and sequence features, - Jalview can display symbols and graphs under the columns of an - alignment, and allow you to mark particular columns of an alignment and add symbols and text - in the annotation area shown below the alignment (which may be hidden if View→Show - Annotation is not ticked). Any displayed annotation row can be hidden (using the pop-up - menu obtained by right-clicking the label), or re-ordered by dragging the label to a new - position with the left mouse button.

-Web services can also add annotation to an alignment (see the JNet and Disorder protein -structure prediction services), and as of Jalview 2.08 quantitative -and symbolic annotations can be added to an alignment via an Annotations File dragged into the -alignment window or loaded from the alignment's file menu. -

Sequence Reference Annotation -

- Sequence reference annotation is created from 3D structure - data, and from the results of sequence based prediction of - secondary structure and disordered region - prediction methods. -

Sequence Group Annotation -

- If sequence groups are defined, Conservation - and Consensus annotation can be enabled - for each group from the Annotations menu, or can - be imported from a Jalview Annotations file. -

Sequence Selection from Annotation -

- Sequences associated with sequence (or sequence group) annotations can be selected by - double-clicking the annotation label with these key combinations: -

double-click - Select associated sequences (replaces current selection)
shift double-click - add sequences to selection
Ctrl (Mac CMD) double-click - toggles inclusion of associated sequences in the current selection

- Note this also works in combination with manual sequence selection in the alignment. -

Interactive Alignment Annotation

-Annotation rows are added using the Annotation Label -menu, which is obtained by clicking anywhere on the annotation row labels -area (below the sequence ID area). -

Add New Row
- Adds a new, named annotation row (a dialog box will pop up for you to - enter the label for the new row).
Edit Label/Description
- This opens a dialog where you can change the name (displayed label), or the description - (as shown on the label tooltip) of the clicked annotation.
Hide This Row
- Hides the annotation row whose label was clicked in order to bring up - the menu.
Hide All <label>
- Hides all annotation rows whose label matches the one clicked. - (This option is only shown for annotations that relate to individual sequences, - not for whole alignment annotations. Since Jalview 2.8.2.)
Delete This Row
- Deletes the annotation row whose label was clicked in order to bring up - the menu.
Show All Hidden Rows
- Shows all hidden annotation rows.
Export Annotation (Application only)
- Annotations can be saved to file or output to a text window in either the - Jalview annotations format or as a spreadsheet style set of comma separated values (CSV).
Show Values in Text Box (applet only)
- Opens a text box with a list of comma-separated values corresponding - to the annotation (numerical or otherwise) at each position in the row. - This is useful to export alignment quality measurements for further analysis. -
Scale Label To Column(introduced in 2.5)
- Selecting this toggles whether column labels will be shrunk to fit within each column, or displayed using the view's standard font size.

-Editing Label and secondary structure Annotation

-Use the left mouse button to select a position along the row that are to -be annotated - these regions will be coloured red. Control and shift in combination -with the left-click will select more than one position, or a range of -positions on the alignment. -

Once the desired position has been selected, use the right mouse -button to open the annotation menu:

Helix
Mark selected positions with a helix glyph (a red -oval), and optional text label (see below). A -dialog box will open for you to enter the text. Consecutive ovals -will be rendered as an unbroken red line. -
Sheet
Mark selected positions with a sheet glyph (a green -arrow oriented from left to right), and optional text label (see -below). A dialog box will open for you to enter the text. Consecutive -arrows will be joined together to form a single green arrow. -
RNA Helix (only shown when working with nucleotide sequences)
-Mark selected positions as participating in a base pair -either upstream or downstream. When the dialog box opens, enter a -'(' to indicate these bases pair with columns upstream (to right), -and ')' to indicate this region pairs with bases to the left of the -highlighted columns.
If any brackets do not match up, then an -orange square will highlight the first position where a bracket was -found not to match. - -
Label
Set the text label at the selected positions. A -dialog box will open for you to enter the text. If -more than one consecutive position is marked with the same label, only -the first position's label will be rendered. -
Colour
Changes the colour of the annotation text label. -
Remove Annotation
Blanks any annotation at the selected positions on -the row. Note: This cannot be undone -

-User defined annotation is stored and retrieved using Jalview Archives. -

Current Limitations

As of version 2.5, the Jalview user interface does not support the -creation and editing of quantitative annotation (histograms and line graphs), or -to create annotation associated with a specific sequence. It is also incapable of -annotation grouping or changing the style of existing annotation (to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an -Annotation file.
-

+ In addition to the definition of groups and sequence features, + Jalview can display symbols and graphs under the columns of an + alignment. These annotation tracks are displayed in the annotation + area below the alignment. The annotation area's visibility is + controlled with the View→Show Annotation + option. +

+ Types of annotation +

Sequence + associated annotation.
Data displayed on sequence annotation + rows are associated with the positions of a sequence. Often this + is 'Reference annotation' such as secondary structure information + derived from 3D structure data, or from the results of sequence + based prediction of secondary + structure and disorder. + If reference annotation is available for a the currently selected + sequences, it can be shown by selecting the Add + Reference Annotation option in the sequence or selection popup + menu.
Group associated annotation.
Data can be associated with + groups defined on the alignment. If sequence groups are defined, Conservation and Consensus annotation can + be enabled for each group from the Annotations menu, or can be + imported from a Jalview Annotations + file.
Alignment associated annotation.
Annotation rows + associated with columns on the alignment are simply 'alignment + annotation'. Controls allow you to interactively create + alignment annotation to add labels and symbols to alignment columns. + Jalview's consensus, conservation and quality calculations also + create histogram and sequence logo annotations on the alignment. +

+ Importing and exporting annotation
+ Annotations on an alignment view are saved in Jalview project files. + You can also load Annotations + Files in order to add any kind of quantitative and symbolic + annotations to an alignment. To see an example, use the Export + Features/Annotation option from an alignment window's File menu. +

+ Layout and display controls
Individual and + groups of annotation rows can be shown or hidden using the pop-up + menu obtained by right-clicking the label. You can also reorder them + by dragging the label to a new position with the left mouse button. + The + Annotations menu provides settings controlling the + ordering and display of sequence, group and alignment associated + annotation. The + Colour by annotation option in the colour menu + allows annotation to be used to + shade the + alignment. Annotations can also be used to + select or + hide columns via the dialog opened from the + Selection menu. +

+ Sequence Highlighting and Selection from Annotation +

+ A single click on the label of an annotation row + associated with sequences and sequence groups will cause the + associated sequences to be highlighted in the alignment view. Double + clicking the label will select the associated sequences, replacing + any existing selection. Like with other kinds of selection, shift + double-click will add associated sequences, and Ctrl + (Mac CMD) double-click will toggle inclusion of associated + sequences in the selection. +

+ Interactive Alignment Annotation +

+ Annotation rows are added using the Annotation + Label menu, which is obtained by clicking anywhere on the + annotation row labels area (below the sequence ID area). +

Add New Row
Adds a new, + named annotation row (a dialog box will pop up for you to enter + the label for the new row).
Edit Label/Description
This + opens a dialog where you can change the name (displayed label), + or the description (as shown on the label tooltip) of the + clicked annotation.
Hide This Row
Hides the + annotation row whose label was clicked in order to bring up the + menu.
Hide All <label>
Hides + all annotation rows whose label matches the one clicked. (This + option is only shown for annotations that relate to individual + sequences, not for whole alignment annotations. Since Jalview + 2.8.2.)
Delete This Row
Deletes + the annotation row whose label was clicked in order to bring up + the menu.
Show All Hidden Rows
Shows + all hidden annotation rows.
Export Annotation (Application + only)
Annotations can be saved to file or + output to a text window in either the Jalview annotations format + or as a spreadsheet style set of comma separated values (CSV). +
Show Values in Text Box (applet + only)
Opens a text box with a list of + comma-separated values corresponding to the annotation + (numerical or otherwise) at each position in the row. This is + useful to export alignment quality measurements for further + analysis.
Scale Label To Column(introduced + in 2.5)
Selecting this toggles whether column + labels will be shrunk to fit within each column, or displayed + using the view's standard font size.

+ Editing labels and secondary structure annotation rows +

+ Use the left mouse button to select a position + along the row that are to be annotated - these regions will be + coloured red. Press Control or shift in + combination with the left-click to either select an additional position, + or a range of positions on the alignment. +

+ Once positions have been selected, use the right + mouse button and select one of the following from the annotation menu: +

Helix
+ Marks selected positions with a helix glyph (a red oval), + and optional text label (see below). A dialog box will open for + you to enter the text. Consecutive ovals will be rendered as an + unbroken red line. +
Sheet
+ Marks selected positions with a sheet glyph (a green arrow + oriented from left to right), and optional text label (see + below). A dialog box will open for you to enter the text. + Consecutive arrows will be joined together to form a single + green arrow. +
RNA Helix (only shown when working with + nucleotide sequences)
Marks selected positions + as participating in a base pair either upstream or downstream. + When the dialog box opens, enter a '(' to indicate these bases + pair with columns upstream (to right), and ')' to indicate this + region pairs with bases to the left of the highlighted columns. + Other kinds of base-pair annotation are also supported (e.g. 'A' + and 'a', or '<' and '>'), and Jalview will suggest an + appropriate symbol based on the closest unmatched + parenthesis to the left.
If any brackets do not match up, then an + orange square will highlight the first position where a bracket + was found not to match. +
Label
+ Set the text label at the selected positions. A dialog box + will open for you to enter the text. If more than one + consecutive position is marked with the same label, only the + first position's label will be rendered. +
Colour
+ Changes the colour of the annotation text label. +
Remove Annotation
+ Blanks any annotation at the selected positions on the row. + Note: This cannot be undone + +

+ User defined annotation is stored and retrieved using Jalview Archives. +

+ Current Limitations +

+ The Jalview user interface does not support interactive + creation and editing of quantitative annotation (histograms and line + graphs), or to create annotation associated with a specific + sequence or group. It is also incapable of annotation grouping or changing + the style of existing annotation (e.g. to change between line or bar + charts, or to make multiple line graphs). These annotation + capabilities are only possible by the import of an Annotation file.
+

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