What is Genome Channel?

The Genome Channel is a series of interface tools for visualization and querying the reference human genome and other genomes assembled and annotated by ORNL and collaborators. It provides access to a variety of computationally generated analyses of genomic DNA sequence collected and assembled from a number of sequencing centers as well as sequences contained in archival public databases. The Genome Channel relies on a number of underlying data resources, analysis tools, and data retrieval methods to provide an up-to-date view of genomic sequences as well as computational and experimental annotation for a variety of organisms.

The Genome Channel Browser

The Genome Channel browser is a java viewer software capable of representing a wide variety of genomic-sequence annotation and links to a large number of related information and data resources. The underlying information and evidence for genes and other features is presented in a variety of graphics windows, text windows, and summary reports.

Browser Views

The Genome Channel browser encompasses a number of views for genome visualization. The views appear on separate windows enabling the user to navigate the genome. The currently supported views are:

• Feature View - provides a detailed zoomed-in view of the contig along with the entire available features analyzed for the contig.
• Sequence View - presents a 10Kb region of the contig's DNA sequence from both strands.

Feature View

The Feature View is launched from the Contig view. It provides a detailed view of the selected contig along with the entire set of the annotated features analyzed for the contig. Each feature is an independent object with its own popup allowing the user the obtain relevant data about the feature. This view is also zoomable allowing the user to inspect a specific region of the contig in much greater detail. The Feature View also provides additional windows for inspecting the reference model and feature data. An example of a Feature View for human chromosome 16, contig TIGR8 is shown here:

The contig is represented as one or more overlapping clones (horizontal colored bars where the color designates the clone source) enclosed by a scalebar at the center of the window. The top half of the window represents the contig's forward strand where the base numbers increase from left to right. The bottom half of the window represents the contig's reverse strand where the direction is from right to left. The window also shows various mapped functional features described in the next section.

This view is also zoomable for greater details. You can zoom into the view using the Options->ZoomIn menu. Alternatively, you can zoom into a region of interest using "rubber-banding" by dragging the mouse while holding down the left button. Each object has a popup menu. You can click on any clone or feature object to obtain its popup menu.

Features

Most features are displayed at either the upper (forward strand) or the lower portion (reverse strand) of the window. However, some features such as repetitive DNA (Rpttv) appear at the center of the window (within the scalebar). For these features, the orientation is shown by a vertical tab ("whisker") which also servers as a handle (i.e., hotspot for clicking, dragging, etc.). The following functional features are supported in the Feature View:

• Repetitive DNA (Rpttv)      - is a repetitive DNA shown as a centrally located blue hollow rectangle with a top or bottom whisker (not shown) and an arrow indicating its orientation. The whisker is its handle and the width of the entire glyph represents the length of the feature.
• Simple Repeat (Smprpt)      - is a simple repeat shown as a centrally located orange hollow rectangle with top and bottom whiskers (not shown) used as handles. The width of the rectangle represents the length of the feature.
• CpG (Cpg)      - is a CpG Island shown as a centrally located magenta hollow rectangle with top and bottom whiskers (not shown) used as handles. The width of the rectangle represents the length of the feature.
• PolyA Site (PolyA)      - is a Polya site shown as a centrally located dark-green hollow rectangle with a top or bottom whisker (not shown) indicating its orientation. The whisker is its handle and the width of the rectangle represents the length of the feature.
• BAC End (BacEnd)      - is a BAC-end fragment shown as a solid arrow (triangle). The BAC-ends are shown on multiple levels at the lower portion of the window where the direction of the arrows indicate their orientation. The colors of the BAC-ends have special meaning. The cyan color () indicates that both pair members exist in the Genome Channel warehouse. The BAC-end pairs that match in a contig are connected by a solid line. A BAC-end shown in yellow () indicates that the other end member does not exist in the warehouse. The red color () indicates that the BAC-end is within 25Kb from the contig end.
• STS (STS)      - is an identified STS marker shown as an orange diamond. The width of the diamond represents the length of the STS.
• Grail Exon (ExonGrail)      - is a Grail exon shown as a solid cyan rectangle. The width of the rectangle represents the length of the exon and its height indicates its score.
• Genscan Exon (ExonGenscan)      - is a Genscan exon shown as a solid blue rectangle. The width of the rectangle represents the length of the exon and its height indicates its score.
• GrailEXP Gene (GeneGrailEXP)      - is a GrailEXP gene shown as one or more solid green rectangles (Grail exons) linked by one or more green horizontal lines (introns). The height of an exon represents its score.
• Genscan Gene (GeneGenscan)      - is a Genscan gene shown as one or more solid brown rectangles (Genscan exons) linked by one or more brown horizontal lines (introns). The height of an exon represents its score.
• Genbank Gene (GeneGenbank)       - is an annotated Genbank entry (CDS) shown as one or more solid red rectangles (exons) linked by one or more red horizontal lines (introns).

Popup Menu

The Feature View popup menu buttons are described below. Note that some of menu items are only applicable to certain objects.

• Summary - Displays summary information on the object on a separate window.
• Sequence - Displays the nucleotide and protein sequence of the object (as applicable) on a separate window:
  • Nucleotide - The object's nucleotide sequence.
  • Protein - The object's translated protein sequence.
• Similarity - Displays the object's protein similarity list.
• Source - Provides a link to the relevant source document for the object and displays it on the web browser.
• Search - Display the search results for:
  • BEAUTY
• Report - Display resports for:
  • Gene Report - Display summary report for the predicted gene.
  • Protein Report - Display summary report for the translated gene.
• Reference Window - Invokes the EST Reference Window for the gene model.

Menubar

The Feature View menubar contains the following options:

• File - The File menu allows you to print and close the view (window). The menu contains the following items:
  • Print - Prints the visible content of the window (currently implemented on secure applets only).
  • Close - Closes and dismisses the window.
• Edit - The Edit menu allows you to edit object data associated with this view. This option is currently implemented on secure applets only.

• Options - The Options menu affects the following options in the view:
  • Hide/Show Labels - Hides or displays all object labels.
  • Hide/Show Toolbar - Hides or displays the toolbar buttons.
  • Hide/Show Titles - Hides or displays the title panel.
  • Hide/Show Rangebar - Hides or displays the rangebar.
  • Hide/Show Bio Popups - Hides or displays the Bio Popups. A Bio Popup is a temporary popup window displaying useful summary information on an object when the mouse is placed over the object.
  • Dark/Light Background - Changes the display background color from light gray to dark blue.
  • Font Size - Changes the font size for all the displayed labels and titles.
  • ZoomIn - Zoom-in the current view.
  • ZoomOut - Zoom-out the current view.
  • Fit - Fit the entire view in the window.

• List - The List menu generates a list of the feature objects in a separate window.

• Features - The Features menu displays a checkbox menu for the available feature objects. By checking or unchecking the feature menu, you can show/hide (load/unload) the feature.

• Windows - The Windows menu generates a separate window for:
  • Features - Displays a separate window listing the data on the feature.
  • Sequence - Invokes the Sequence View.

The Feature View toolbar contains the following buttons:

	Zoom-in the current view (same as Options->ZoomIn).
	Zoom-out the current view (same as Options->ZoomOut).
	Fit the entire view in the window (same as Options->Fit).
	Toggle show/hide the Bio Popups(same as Options->Show/Hide Bio Popups).
	Toggle show/hide (load/unload) the BAC-ends (same as Features->Bac End).
	Toggle show/hide (load/unload) the simple repeats (same as Features->SmpRpt).
	Toggle show/hide (load/unload) the repetitive DNAs (same as Features->Rpttv).
	Toggle show/hide (load/unload) the PolyA sites (same as Features->PolyA).
	Toggle show/hide (load/unload) the CpG islands (same as Features->Cpg).
	Toggle show/hide (load/unload) the Genbank genes (same as Features->Genbank Gene).
	Toggle show/hide (load/unload) the Genscan gene models (same as Features->Genscan Gene).
	Toggle show/hide (load/unload) the GrailEXP gene models (same as Features->GrailEXP Gene).
	Toggle show/hide (load/unload) the STS markers (same as Features->STS).
	Toggle show/hide (load/unload) the clones (same as Features->Clone).
	Print the view (same as File->Print).
	Show overview help (same as Help->Overview).

The Sequence View is launched from the Feature View. It is a scrollable window which shows 10K bases of the contig's DNA sequence from both strands. The loaded features from the Feature View is also mapped and shown on this window. An example of a Sequence View for human chromosome 16, contig TIGR8 is shown here:

To view a different sequence region in the Sequence View, place the cursor inside the slider-box in the Feature View (the cursor changes to "move-cursor") and drag the box to the desired location while holding down the left button. Along with the slider-box, a slidable red gauge-bar ("slider-gauge") is also displayed in the Feature View. The width of the slider-gauge represents the viewing area in the Sequence Window. Similar to the slider-box, you can slide the slider-gauge to a different location in the Feature View which will cause the Sequence View to scroll to that location. Conversely, by scrolling the Sequence View, the slider-gauge will move to the corresponding location in the Feature View.

Sequence View Features

The features which are loaded and viewable in the parent Feature View are also displayed in this window. The features are displayed as a solid bar (same colors as in the Feature View) at either the upper (forward strand), the lower portion (reverse strand), or the center of the window. The location of a feature corresponds to its location in the Feature View. The functional features are:

• Repetitive DNA (Rpttv)      - is a repetitive DNA shown as a centrally located blue rectangle.
• Simple Repeat (Smprpt)      - is a simple repeat shown as a centrally located orange rectangle.
• CpG (Cpg)      - is a CpG Island shown as a centrally located magenta rectangle.
• PolyA Site (PolyA)      - is a Polya site shown as a centrally located dark-green rectangle.
• STS (STS)      - is an identified STS marker shown as an orange rectangle.
• Grail Exon (ExonGrail)      - is a Grail exon shown as a solid cyan rectangle.
• Genscan Exon (ExonGenscan)      - is a Genscan exon shown as a solid blue rectangle.
• GrailEXP Gene (GeneGrailEXP)      - is a GrailEXP gene shown as one or more solid green rectangles (Grail exons) linked by one or more green horizontal lines (introns).
• Genscan Gene (GeneGenscan)      - is a Genscan gene shown as one or more solid brown rectangles (Genscan exons) linked by one or more brown horizontal lines (introns).
• Genbank Gene (GeneGenbank)       - is an annotated Genbank entry (CDS) shown as one or more solid red rectangles (exons) linked by one or more red horizontal lines (introns).

Menubar

The Sequence View menubar contains the following options:

• File - The File menu allows you to print and close the view (window). The menu contains the following items:
  • Print - Prints the visible content of the window (currently implemented on secure applets only).
  • Close - Closes and dismisses the window.

• Options - The Options menu affects the following options in the view:
  • Hide/Show Toolbar - Hides or displays the toolbar buttons.
  • Hide/Show Bio Popups - Hides or displays the Bio Popups. A Bio Popup is a temporary popup window displaying useful summary information on an object when the mouse is placed over the object.

The Sequence View toolbar contains the following buttons:

	Toggle show/hide the Bio Popups(same as Options->Show/Hide Bio Popups).
	Print the view (same as File->Print).
	Show overview help (same as Help->Overview).