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.
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
- 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
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
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
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
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.
Once a region is displayed, you can navigate through it in a number of
- 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
- 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
- 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 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
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.
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:
You can have as many "add" options as you like:
The format is:
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:
This says to configure the "MyDeletions" track with the following options:
See the uploaded annotation help
file for more details.
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.
Lincoln Stein <email@example.com>
2008.The servers are free for academic use. Please contact IPR Cell for commercial use. All third party trademarks are owned by their respective owners and used with permission
FishMap development has been generously funded by the Council for Scientific and Industrial Research (CSIR), India (Grant No FAC002)
FishMap is hosted and maintained at the G N Ramachandran Knowledge Center for Genome Informatics at the Institute of Genomics and Integrative Biology
No information is shared.
Generic genome browser version 1.70