Selecting Regions Overview Panel Detail Panel Adding Annotations Quick Uploads

Generic Genome Browser: General Help

These are general instructions for using the Generic Genome Browser. This page should be customized by the administrator of this resource to describe site-specific features.

Selecting a Region of the Genome

To select a region of the genome to view, enter its name in the text field labeled "Landmark or Region". Recognized types of names are under the control of the administrator, but usually the following names are accepted:

a chromosome name
For genomes that have been assembled into chromosome-length segments, you can enter the name of the chromosome. The chromosome name follows the conventional nomenclature for the species. For example, C. elegans chromosomes are indicated using roman numerals, such as III, D. melanogaster uses chromosome arms such as 2L and 2R, while H. sapiens uses arabic numbers such as 9.

a gene name
You can enter the name of a gene using the standard nomenclature for that species.

a contig or clone name
You can enter the name of a structural landmark such as a cosmid, BAC or contig.

an accession number
You can enter a GenBank or EMBL accession number.

protein names, primer names, ORF IDs, author names...
At the discretion of the administrator of the database, other identifiers can be entered. See the examples listed at the top of the browser page for hints.

The Overview and Detail Panels

If the landmark is found in the database, the browser will display the region of the genome it occupies. The region is displayed in two graphical panels:

overview panel
This panel displays the genomic context, typically an entire assembled chromosome or a large portion of the sequence assembly such as a scaffold or contig. At the administrators' discretion, certain important landmarks, such as a well-known genetic markers or cytogenetic bands can be placed in this view. A red rectangle indicates the region of the genome that is displayed in the detail panel. This rectangle may appear as a single line if the detailed region is relatively small.

detail panel
This panel displays a zoomed-in view of the genome corresponding to the overview's red rectangle. The detail panel consists of one or more tracks showing annotations and other features that have been placed on the genome. The detail panel is described at length later.

If the requested landmark is not found, the browser will display a message to this effect.

Specifying the Landmark Class

At the administrator's option, some kinds of landmarks may have to be qualified with their "class" using the format class:landmark. For example, to look up the PCR product sjj_K08A8.1 in the C. elegans database, you will search for PCR_Product:sjj_K08A8.1.

In the case of clashes between names, such as a contig and a gene both named c23, you can use the name class to specify which landmark you mean.

Viewing a Precise Region around a Landmark

You can view a precise region around a landmark using the notation landmark:start..stop, where start and stop are the start and stop positions of the sequence relative to the landmark. The beginning of the feature is position 1. In the case of complex features, such as genes, the "beginning" is defined by the database administrator. For example, in the C. elegans data set, position 1 of a predicted gene is the AUG at the beginning of the CDS, so to view the region that begins 100 base pairs upstream of the AUG ends 500 bases downstream of it, you would search for mek-1:-99..500.

This offset notation will work correctly for negative strand features as well as positive strand features. The coordinates are always relative to the feature itself.

To offset relative to a qualified feature name, just include the type name, as in PCR_Product:sjj_K08A8.1:-500..500 (note that this particular example only works with the C. elegans database).

Searching for Keywords

Anything that you type into the "Landmark or Region" textbox that isn't recognized as a landmark will be treated as a full text search across the feature database. This will find comments or other feature notations that match the typed text. Depending on how the database is set up, you may find gene names, gene functions, author names, or bibliographic references.

If successfull, the browser will present you with a list of possible matching landmarks and their comments. You will then be asked to select one y to view. To see this in action, try typing "kinase" into the "Landmark or Region" box.

Navigation

Once a region is displayed, you can navigate through it in a number of ways:

Scroll left or right with the <<, <, > and >> buttons
These buttons, which appear in the "Scroll/Zoom" section of the screen, will scroll the detail panel to the left or right. The << and >> buttons scroll an entire screen's worth, while < and >> scroll a half screen.

Zoom in or out using the "Show XXX Kbp" menu.
Use menu that appears in the center of the "Scroll/Zoom" section to change the zoom level. The menu item name indicates the number of base pairs to show in the detail panel. For example, selecting the item "100 Kbp" will zoom the detail panel so as to show a region 100 Kbp wide.

Make fine adjustments on the zoom level using the "-" and "+" buttons.
Press the - and + buttons to change the zoom level by small increments (usually 10-20%, depending on how the browser is configured).

Recenter the detail panel by clicking on its scale
The scale at the top of the detail panel is live. Clicking on it will recenter the detail panel around the location you clicked. This is a fast and easy way to make fine adjustments in the displayed region.

Get information on a feature by clicking on it
Clicking on a feature in the detail view will link to a page that displays more information about it. This could be a page on the browser's web site, or a page on an external web site.

Jump to a new region by clicking on the overview panel
Click on the overview panel to immediately jump to the corresponding region of the genome.

The Detail Panel

The detailed view is composed of a number of distinct tracks which stretch horizontally from one end of the display to another. Each track corresponds to a different type of genomic feature, and is distinguished by a distinctive graphical shape and color.

The key to the tracks is shown at the bottom of the detail panel. For more information on the source and nature of the track, click on the track label in the "Search Settings" area (discussed below).

Customizing the Detail Panel

You can customize the detailed display in a number of ways:

Turn tracks on and off using the "Search Settings" area

The panel labeled "Search Settings" contains a series of checkboxes. Each checkbox corresponds to a track type. Selecting the checkbox activates its type. Select the label to the right of the checkbox to display a window that provides more detailed information on the track, such the algorithm used to generate it, its author, or citations.

Change the properties of the tracks using the "Set Track Options" button

This will bring up a window that has detailed settings for each of the tracks. Toggle the checkbox in the "Show" column to turn the track on and off (this is the same as changing the checkbox in the Search Settings area). Change the popup menu in the "Format" column to alter the appearance of the corresponding track. Options include: Compact which forces all items in the track onto a single overlapping line without labels or descriptions; Expand, which causes items to bump each other so that they don't collide; and Expand & Label, which causes items to be labeled with their names and a brief description. The default, Auto will choose compact mode if there are too many features on the track, or one of the expanded modes if there is sufficient room. Any changes you make are remembered the next time you visit the browser. Press Accept Changes and Return... when you are satisfied with the current options.

Change the order of tracks using the "Set Track Options" button
The last column of the track options window allows you to change the order of the tracks. The popup menu lists all possible feature types in alphabetic order. Select the feature type you wish to assign to the track. The window should refresh with the adjusted order automatically, but if it doesn't, select the "Refresh" button to see the new order.

Uploading Your Own and 3d Party Annotations

This browser supports third party annotations, both your own private annotations and published annotations contributed by third parties.

Uploading Your Own Annotations

To view your own annotations on the displayed genome, go to the bottom of the screen and click on the Browse... button in the file upload area. This will prompt you for a text file containing your annotations. See the annotation format help document for information on how to create this file.

Once loaded, tracks containing these annotations will appear on the detailed display and you can control them just like any of the built-in tracks. In addition new Edit, Delete and Download buttons will appear in the file upload area. As their names imply, these buttons allow you to edit the uploaded file, download it, or delete it completely.

The date at which the uploaded file was created or last modified is printed next to its name. If there are a manageable number of annotated areas, GBrowse will create links that allow you to jump directly to them.

You may upload as many files as you wish, but be advised that the performance of the browser may decrease if there are many large uploads to process.

Viewing 3d Party Annotations

To view 3d party annotations, the annotations must be published on a reachable web server and you must know the annotation file's URL.

At the bottom of the browser window is a text box labeled "Enter Remote Annotation URL". Type in the URL and then press "Update URLs". The system will attempt to upload the indicated URL. If successful, the data will appear as one or more new tracks. Otherwise you will be alerted with an error message.

You may add as many remote URLs as you wish. To delete one, simply erase it and press "Update URLs" again.

Quick Uploads

Another way to upload your own features is by adding an "add" argument to the gbrowse URL. For example, this URL will create a track named "MyDeletions" containing a feature named "Deletion3". Deletion3 occupies the region on chromosome 3 between 10,050,000 and 10,051,000:

https://tomato.biodesign.asu.edu/cgi-bin/gbrowse/celegans_WS250/?add=chr3+MyDeletions+Deletion3+10050000..10051000

You can have as many "add" options as you like:

https://tomato.biodesign.asu.edu/cgi-bin/gbrowse/celegans_WS250/?add=chr3+MyDeletions+Deletion3+10050000..10051000;add=chr3+MyDeletions+Deletion4+950000..960000

The format is:

reference+trackName+featureName+start..stop,start..stop,start..stop ...

where "reference" is the name of the landmark that start and stop are relative to. You can use a chromosome name, a contig name, a gene name, or anything else that this browser recognizes in the search box. "trackName" is the name of the track to upload, "featureName" is the name of the feature you are uploading, and "start..stop" are the start and end coordinates relative to "reference". For multisegmented features, specify multiple start..stop pairs separated by commas.

For more control over the way quick upload features appear, specify the "style" option to the URL:

https://tomato.biodesign.asu.edu/cgi-bin/gbrowse/celegans_WS250/?style=MyDeletions+glyph=arrow+double=1+fgcolor=blue

This says to configure the "MyDeletions" track with the following options: 

glyph=arrow
double=1
fgcolor=blue

See the uploaded annotation help file for more details

.

Software Bugs

As always, this software may contain bugs. Please report any that you suspect to the author, along with whatever information that you can provide as to what you were doing when the bug appeared.

AUTHOR

Lincoln Stein <lstein@cshl.org>

 

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Generic genome browser version 1.70