The name of the project. This can be changed at the top of the Project Page.

The ID for the project and map.

The date and time the project was created.

The date and time the project was last saved. This date is used to calculate when to delete old session projects.

The total size of the project, including all the jobs.

The total length of the map sequence. If any contigs have been marked as invisible, then both the total and visible length will be shown.

The number of contigs in the project. If any contigs have been marked as invisible, then both the total and visible number will be shown. Clicking on the contig count will open the Contig Panel.

The number of features in the project. Clicking on the feature count will open the Feature Panel.

The number of plots in the project. Clicking on the plot count will open the Plot Panel.

The number of bookmarks in the project. Clicking on the bookmark count will open the Bookmark Panel.

The number of tracks in the project. Clicking on the track count will open the Track Panel.

The number of legend items in the project. Clicking on the legend count will open the Legend Panel.

The number of captions in the project. Clicking on the caption count will open the Caption Panel.

The number of jobs in the project. Clicking on the job count will open the Job Panel.

The number of snapshots in the project. Clicking on the snapshot count will open the Snapshot Panel.

The source of the data used to create the project: genome, reads, json, example, snapshot, tutorial, api

The project level genetic code. This is used as the default when translating proteins.

Use the mouse scroll wheel to zoom directly on the map. The zoom position is based on the mouse location.

Click and drag to move/pan the map position.

Clicking an element (e.g. feature, captions, legend items) will open the corresponding panel in the Sidebar and open the details for the element.

Hovering over an element (e.g. feature, contigs, plots) will show a popup with information for that element.

If a legend is displayed, the color swatches can be clicked to bring up the Color Picker.

[ . ] Reset the map position and zoom level.

[↓] Zoom in on the map.

[↑] Zoom out on the map.

[→] Move clockwise/right along the map.

[←] Move counter-clockwise/left along the map.

[ / ] Set the map format to circular.

[ / ] Set the map format to linear.

Invert all the colors on the map.

Toggle the legend on/off.

Toggle the default labels on/off. (Best for maps with many evenly distributed labels)

Toggle the angled labels on/off. (Best for maps with fewer labels or with labels that are clustered together)

Lock the aspect ratio of the map to a square.

Close the Sidebar

Open the Sidebar

Add a new Track.

Track is visible or not visible.

Delete the Track. A dialog will provide options to delete features and/or legends that are exclusive to the track being deleted.

The name of the track.

The position of the track relative to the backbone:

• Both: the forwards strands/slots will be on the outside of the backbone while the reverse strands will be on the inside
• Inside: all the strands/slots will be on the inside of the backbone.
• Outside: all the strands/slots will be on the outside of the backbone.

Method for separating features onto track slots:

• None: The features are not separated and all appear on 1 slot.
• Strand: The features will appear on 2 slots. One slot each for the forward and reverse strands.
• Reading Frame: The features will appear on 6 slots. One slot each for each reading frame.
• Type: The features will appear on n slots where n is the number of types. One slot each for each type. Slots are sorted so the most common type is first.
• Legend: The features will appear on n slots where n is the number of legends. One slot each for each legend. Slots are sorted so the most common legend is first.

The size ratios all depend on each other. For example:

• If all the track ratios are the same then all the track slots will be the same width.
• If one track has a ratio of 2 and all the others are 1, then it will be 2 times wider than the others.
• If one track has a ratio of 2 and all the others are 0.5, then it will be 4 times wider than the others.

This track contains features with a source, type or tag equal to one of the provided values. See Track Features for details and examples.

The number of features or plot points that this track contains. Clicking the count will take you to the Feature Panel.

Items placed on the map are not static and move when the map is panned or zoomed. The map position is based on the Length Percent of the genome sequence (e.g. 50% would be at the map half way point) and the Offset is a distance from the map. Positive Offsets indicate a distance from the outside ring of the map while a negative Offset indicates a distance from the inner ring of the map.

The canvas is static and can be thought of as the window through which the map is viewed. Items placed on the canvas do not move when the map is panned or zoomed. The canvas position can be quickly set by clicking one of the areas in the 9 rectangle grid (e.g. upper-left). Fine tuning of the position can be done with the X/Y Percent inputs.

When the legend is positioned on the map, this button will move the map to show the legend. This button does not appear when positioned on the Canvas.

Track is visible or not visible.

Where to place the legend. See Legend/Caption Positions for details.

• Canvas: Legend is static and does not move.
• Map: Legend moves with the map.

The anchor point describes where the position attaches to the legend/caption bounding box.

The default font to use for the legend items. Individual items can override this value. The alignment buttons will align the all the legend items:

• Left: the color swatches will be on the left
• Right: the color swatches will be on the right

The default color to use for the legend items. Individual items can override this value.

The default minimum arc length to use for the legend items. Individual items can override this value. Features are drawn based on their length and therefore small features (e.g. 1 bp) can appear invisible on maps depending on the zoom level. By setting a minimum arc length, small features will be more visible and be darker on the map.

The color to use for the legend background.

Draw features as arrows. The arrow head length can be adjusted LINK.

Draw features as arcs

Draw features as arcs with the width of the arc set to the feature score. The score should be between 0 and 1, where 0 would be 0 width and 1 would be full width. If no score is associated with the feature it will be drawn full width.

Do not draw features

Add a new legend item.

Legend item is visible or not visible.

Delete the legend item. A dialog will provide options to delete features and/or plots that are exclusive to the legend being deleted.

The name of legend item as it will appear in the legend. Names must be unique.

The color to use when drawing features or plots with this legend item.

The decoration to use when drawing features. See Decorations table.

• Arrow - Draw features as arrows.
• Arc - Draw features as arcs.
• Score - Draw as arc with width based on feature score (0-1).
• None - Do not draw feature.

The font to use for this legend item. The font options will be faded, if the default is being used. If changed, this value will override the default. Click the Default button to use the Legend default.

The font color to use for this legend item. The font color will be faded, if the default is being used. If changed, this value will override the default. Click the Default button to use the Legend default.

Features are drawn based on their length and therefore small features (e.g. 1 bp) can appear invisible on maps depending on the zoom level. By setting a minimum arc length, small features will be more visible and be darker on the map. The minimum arc length will be faded, if the default is being used. If changed, this value will override the default. Click the Default button to use the Legend default.

Add a new caption.

When the caption is positioned on the map, this button will move the map to show the caption. This button does not appear when positioned on the Canvas.

Caption is visible or not visible.

Delete the caption.

The text to display as a caption on the map. Multiple lines of text can be used.

Where to place the caption. See Legend/Caption Positions for details.

• Canvas: Caption is static and does not move.
• Map: Caption moves with the map.

The anchor point describes where the position attaches to the legend/caption bounding box.

The font to use for the caption. The alignment buttons only matter when using multiple lines of text.

The color to use for the caption.

The color to use for the caption background.

This selected map component (e.g. labels, ruler, backbone, dividers, sequence) will be visible/invisible.

The background color for the map.

With feature shading on, features and the backbone are drawn with a slight bevel effect to add 3D depth.

The length of the arrow on features that have the Arrow decoration. The length is based on the feature width and can range from 0 (no arrowhead) to 1 (the arrowhead is as long as the feature is wide).

The initial thickness of the map at a zoom level of 1. This value is a proportion of the canvas size. For circular maps, this is defined as the proportion of the smallest canvas dimension. For linear maps, it's the proportion of the canvas height. This value is ignored if the maximum map thickness is smaller.

The maximum thickness of the map when zoomed in. This value is a proportion of the canvas size. For circular maps, this is defined as the proportion of the smallest canvas dimension. For linear maps, it's the proportion of the canvas height.

The font color to use for all the labels. The default is to use the same color as the feature's current legend.

The font to use for the labels.

If set to Yes, then only features marked as favorites will have labels.

The colo/cr to use for the ruler lines and text.

The font to use for the ruler labels.

The color to use for the center line.

The thickness/width of the center line.

The center line dash pattern. A comma separated list of numbers that specify distances to alternately draw a line and a gap. If the number of elements in the list is odd, the elements of the list get copied and concatenated. For example, [5, 15, 25] will become [5, 15, 25, 5, 15, 25]. For a solid line, provide an empty list.

The color to use for the backbone.

If contigs are present, this is the color for alternating contigs.

The thickness/width of the backbone. The backbone will automatically get thicker when zoomed in to show the sequence.

The decoration to use when drawing contigs:

• Arrow - Draw contigs as arrows.
• Arc - Draw contigs as arcs.

The color to use for the divider.

Turn on/off divider mirroring:

• On: use same settings for track and slot dividers.
• Off: use different settings for track and slot dividers.

The thickness of the divider.

The spacing between the slot/track contents and the divider.

The color to use for the sequence.

The font to use for the sequence.

Move and zoom to focus on this contig.

Contig is visible or not visible. At least one contig must be visible.

Delete the contig. If there is only one contig, it can not be deleted.

The name for the contig. Contig names must be unique and contain only letters, numbers, and underscores. All other characters (e.g. -.+:|) will be removed. As contig names may be used when running tools, changing the contig name may affect job results.

The order of the contig in relation to the other contigs. Changing this number will move the contig around the map. All the features associated with the contig will move with it.

The direction of the contig. Flipping the orientation will also flip the features on the contig.

By default contigs will use the Backbone color and alternate color. Change this value to make a contig stand out.

The number of features on this contig. Clicking on the feature count will open the Feature Panel.

Add a new feature.

Mark this feature as a favorite. This can be useful when combined with the Labels - Only Favorites setting.

Move and zoom to focus on this feature.

The feature is visible or not visible.

Delete the feature.

The name for the feature.

The feature type (e.g CDS, tRNA, rRNA). If the project was started with a GenBank file, the type will be same as the feature key. Feature keys are described in detail here.

To create a new type, check the feature's checkbox and then click the edit (pencil) button.

The Legend to use when drawing this feature. The legend describes the feature color and decoration.

The start position (bp) in relation to the contig the feature is on. Not shown for features with multiple locations.

The stop/end position (bp) in relation to the contig the feature is on. Not shown for features with multiple locations.

The locations (as start/stop pairs) of this feature in relation to the contig the feature is on. Locations indicate muliple regions should be joined to form one contiguous sequence. Locations can not be edited at this time.

The strand the feature is on.

Length of the feature.

Score associated with the feature. This is a number between 0 and 1. The score can be used by the legend decoration to alter the feature width.

The Source ID is added to the feature by the tool that created the feature. This provides an easy way to add all the features created by a tool to a track.

The contig this feature is on. If the project contains multitple contigs, this contig can be changed to a different contig. Warning: if the feature position will not fit within the selected contig, the feature start/stop will be altered to fit.

Tags are a simple way to label or group features. Multiple tags are allowed.

A list of the Tracks this feature is currently on. Clicking the track name will open the appropriate track.

The sequence of the feature. Only the first 1000 nucleotides/amino acids are shown. CDS and ORF features have the option to show the translated sequence. If the feature has a translation different from that derived from the sequence, a note will be displayed under the sequence. Use the copy button to copy the entire sequence to the clipboard.

Add a new plot. Brings up the dialog for the Plots tool.

Mark this plot as a favorite.

The plot is visible or not visible.

Delete the plot.

The name for the plot.

The Legend to use when drawing the plot above the baseline.

The Legend to use when drawing the plot below the baseline. Setting this to Same as Above will result in a single color for the plot.

The baseline for the plot. The plot is filled with the appropriate legend color from the plot value to the baseline.

The minimum value to use for the axis. This number can not be greater than the minimum value.

The maximum value to use for the axis. This number can not be less than the maximum value.

The number of points along this plot.

The minimum value of this plot.

The maximum value of this plot.

The average value of this plot.

The median value of this plot.

The Source ID is added to the plot by the tool that created the plot.

A list of the Tracks this plot is currently on.

The plot type. There is currently only the line type.

Add a new bookmark. The Mark button in the Location Bar can also be used.

Move and zoom to the bookmark's saved position. Depending on the bookmark, the map format may also change.

Delete the bookmark.

The name for the bookmark. Defaults to Bookmark-n, where n is an incrementing number starting with 1.

A single keyboard key that when pressed quickly moves to this bookmark. By default, bookmarks will assigned numbers: 1, 2, 3, etc

The map format: Linear or Circular

The map position in base pairs.

The zoom level.

A zero offset means the map should be centered on the backbone. Positive and negative values move the backbone from the canvas center.

Restore the snapshot to the current project. The previous map state (before applying the snapshot) can be recovered by clicking the Revert Changes button.

Copy a link to the snapshot. The link can be shared with others so they can view the snapshot as a new project. Sharing must be enabled for the snapshot to be viewed by others.

Download the snapshot as a Map JSON file.

Mark this snapshot as a favorite.

Delete the snapshot. Share links to the snapshot will no longer work.

Refreshes the list of snapshots. This is not normally needed, however, if you expect to see snapshots in the list and there are none, try clicking this button.

The name for the snapshot. Defaults to snapshot-1, snapshot-2, etc.

A unique id for the snapshot. This id is used for sharing of the snapshot. Anyone with this ID will have access to this snapshot if sharing is enabled.

By default snapshots are not shared. While sharing is on, anyone with the snapshot ID will be able to create a new project based on the the snapshot map JSON. Jobs for the project are never shared.

The number of times this snapshot has been viewed by others. In other words, the number of times the snapshot ID has been used to create a new project.

The size of the snapshot (ie. Map JSON file). Snapshots count towards the user's storage limit.

Date and time the snapshot was created.

Short description of the tool.

This is the software and version number for any external software packages used in this tool. Clicking on this will open the software home page in a new tab.

Citation to use for external software packages. Clicking on this will open the publication in a new tab.

The internal Proksee version for this tool. This will change with software package updates as well as any changes to the Proksee wrapping code. Clicking on this will open the tool summary page in a new tab. The summary includes the change log.

Refreshes the list of job. This is not normally needed, however, if you expect to see jobs in the list and there are none, try clicking this button.

Brings up a dialog to add the results to the map.

Expands the Job to a new Job Tab in the Project Tabs list.

Marks this job as a favorite. Favorited jobs will automatically have their Job Tab open the next time the project page is loaded.

Deletes this job from the server. Note that the CGView Builder jobs can not be deleted.

The name for this job. Click on the name to edit it.

One of the following: queued, running, complete or failed. Job are typically done in minutes but some may take hours. If your job has been queued or running for longer than 24 hours, or if you keep getting an error, please Contact Us with the Project ID, Job ID and a description of the problem.

Total size of the job.

The job ID. Provide this ID and the project ID when contacting support.

The source prefix added to any features created from this job. Each time features are added to a map from the same job, the number will increase (e.g. card-1.1, card-1.2). Clicking on the ID will open the Feature Panel and search for all features from this job.

The day and time this job was submitted.

The day and time this job started running.

The day and time this job finished running.

The time it took to run the job not including queue time.

The number of days before this job is deleted. Only shown for session projects.

The inputs used to run the job. This will include your settings from the dialog used to start the job.

Download this file.

Cycles backward and forward through the selected files. Only available when multiple files are selected.

Open the settings popup for the currently selected file type. This usually contains settings for fonts and other display options.

Opens the file viewer full screen, hiding the file tree.

Opens the file viewer to the bottom of the file tree.

Opens the file viewer to the right of the file tree.

One of the following font families. Note, that the actual font used will depend on your device and browser.

• Sans Serif: plain font that has no "serifs" (ie. the little strokes on the end of the letters).
• Serif: font with "serifs" (ie. the little strokes on the end of the letters).
• Monospace: font where each character and space has the same width.

Style for the font. Bold, italic or both

Size of the font in pixels.