=head1 gbrowse_img - CGI script to generate genome images via the Generic Genome Browser
Will generate this picture:
Will return this document:
Will return this document:
## Feature types for source yeast
Genes Named gene default
ORFs ORF default
tRNAs tRNAs default
LTRs Long Terminal Repeats
TranslationF 3-frame translation (forward)
TranslationR 3-frame translation (reverse)
ncRNA Noncoding RNAs
This CGI script is an interface to the Generic Genome Browser for the
purpose of retrieving dynamic images of a region of the genome. It can
be used as the destination of an tag like this:
The script can also be used to superimpose one or more external
features onto the display, for example for the purpose of displaying
BLAST hits, an STS or a knockout in the context of the genome.
=head1 CGI arguments
The script recognizes the following CGI arguments, which can be passed
either as GET or POST argument=value pairs. Argument pairs must be
separated by semicolons (preferred) or by ampersands.
Argument Alias Description
name q genomic landmark or range
type t tracks to include in image
width w desired width of image
options o list of track options (compact, labeled, etc)
abs b display position in absolute coordinates
add a added feature(s) to superimpose on the image
style s stylesheet for additional features
keystyle k where to place the image key
overview force an overview-style display
flip f flip image left to right
embed generate full HTML for image and imagemap for use in an
format format for the image (use "SVG" for scaleable vector
list get certain types of configuration information
source database name
The arguments are explained in more detail here
=item name (Alias: q)
This argument specifies the region of the genome to be
displayed. Several forms are recognized:
Display the landmark named "Landmark". Valid landmark names include
chromosomes, contigs, clones, STSs, predicted genes, and any other
landmark that the administrator has designated. Be careful when
fetching large landmarks such as whole chromosomes!
Display the region between start and end relative to "Landmark".
Display "Landmark", restricting to a particular class, such as
"PCR_Product". The list of classes is under the control of the
database administrator and is not yet available through this
As above, but restricted to the designated range.
If you use multiple name options, then this script will generate an
overview image showing the position of each landmark. The alias "q"
can be used to shorten the length of the URL.
=item type (Alias: t)
This argument lists the feature types to display. The value of this
argument is a list of track names separated by spaces ("+" characters
when URL-escaped). For example:
Multiple type= arguments will be combined to form a single
space-delimited list. The alias "t" can be used to shorten the length
of the URL.
If the track name has a space in it, put quotes around the name:
=item width (Alias: w)
Width of the desired image, in pixels.
=item options (Alias: o)
A space-delimited list ("+" characters when URL-escaped) of
mnemonic/option pairs describing how features should be formatted.
Options are integers from 0 to 3, where 0=auto, 1=compact, 2=expanded,
3=expanded and labeled. For example, to specify that the tRNA and NG
tracks should always be expanded and labeled, but that the WABA track
should be compact, use:
The alias "o" can be used to shorten the length of the URL.
Use absolute (chromosome) coordinates when displaying the image. An
argument of abs=1 will turn on absolute coordinate addressing. An
argument of abs=0 will use relative coordinate addressing (this is the
=item add (Alias: a)
Superimpose one or more additional features on top of the view.
Features are specified as space ("+") delimited lists in the following
"Landmark" is the landmark name, "Type" is a descriptive type that
will be printed in the image caption, "Name" is a name for the feature
to be printed above it, and start..end is a comma-delimited list of
ranges for discontinuous feature. Names that contain white space must
be quoted, for example "BLAST hit". Note that this all has to be
URL-escaped, so an additional feature named "Your Sequence", type
"Blast Hit", that is located on chromosome III in a gapped range
between 20000 and 22000, will be formatted as:
One or both of the type and name can be omitted. If omitted, type will
default to "Your Features" and the name will default to "Feature XX"
where XX is an integer. This allows for a very simple feature line:
Multiple add= arguments are allowed. The alias "a" can be used to
shorten the length of the URL.
The style argument can be used to control the rendering of additional
features added with "add". It is a flattened version of the style
configuration sections described in this document For example, if
you have added a "Blast Hit" annotation, then you can tell the
renderer to use a red arrow for this glyph in this way:
=item keystyle (Alias: k)
Controls the positioning of the track key. One of "right", "left",
"between" (default) or "bottom"
Ordinarily the image will show the detail panel if the query region
corresponds to a single region, and the overview panel if multiple
regions match (or if a region that is too large to show
matches). Setting overview=1 will force the overview to be shown in
=item flip (Alias: f)
Flip the image left to right. Arguments are 0=don't flip (default),
Generate image and a corresponding HTML imagemap in a form suitable
for embedding into a frame.
=item highlight (Alias: h)
Highlight (in yellow) all features whose names match the indicated
Specify the format for the image file. Either "GD" (the default) or
"GD::SVG" for scaleable vector graphics.
If this argument is present, it will cause the script to dump out
various types of information in plain text form. Currently the two
values for this argument are sources, to dump out the list of data
sources, and types, to dump out the list of configured types. For
list=sources, the script will return a simple text list of the data
source names. For list=types, the script will return a three-column
tab-delimited list giving the track names and feature types
corresponding to the currently-selected data source. The format is as
Mnemonic Full description of feature [default]
The third column contains the word "default" if the track will be
shown by default when no type argument is provided.
This argument specifies the database for the images. The list of
sources can be found using list=sources.
Putting it all together, here's a working (very long) URL:
If you wish to associate the image with an imagemap so that clicking
on a feature takes the user to the destination configured in the
gbrowse config file, you may do so by placing the URL in an