<img src="http://www.wormbase.org/db/seq/gbrowse_img/wormbase?name=mec-3;width=400">
Will generate this picture:
<a href="http://www.wormbase.org/db/seq/gbrowse_img?list=sources">list</a>
Will return this document:
## Sources human ws77 worm_pmap embl fly briggsae yeast wormbase
<a href="http://www.wormbase.org/db/seq/gbrowse_img?list=types">types</a>
Will return this document:
## Feature types for source yeast
Genes Named gene default
ORFs ORF default
CDS CDS
tRNAs tRNAs default
Centro Centromeres
Transp Transposons
LTRs Long Terminal Repeats
TranslationF 3-frame translation (forward)
DNA/GC Content
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 <img> tag like this:
<img src="http://www.wormbase.org/db/seq/gbrowse_img/wormbase?name=III:1 ..1000">
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.
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
embedded frame
format format for the image (use "SVG" for scaleable vector
graphics)
list get certain types of configuration information
source database name
The arguments are explained in more detail here
name=Landmark
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!
name=Landmark:start..end
Display the region between start and end relative to ``Landmark''.
name=Class: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 interface.
name=Class:Landmark:start..end
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.
<img src="http://www.wormbase.org/db/seq/gbrowse_img/wormbase?name=mec-3;
type=tRNA+NG+WABA+CG+ESTB">
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:
type="microbe tRNA"+NG+WABA+CG+ESTB
options=tRNA+3+NG+3+WABA+1
The alias ``o'' can be used to shorten the length of the URL.
add=Landmark+Type+Name+start..end,start..end,start..end
``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:
add=III+%22Blast%20Hit%22+%22Your%20Sequence%22+20000..21000,21550..22000
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:
add=III+20000..21000,21550..22000
Multiple add= arguments are allowed. The alias ``a'' can be used to shorten the length of the URL.
Mnemonic <tab> Full description of feature <tab> [default]
The third column contains the word ``default'' if the track will be shown by default when no type argument is provided.
Putting it all together, here's a working (very long) URL:
http://www.wormbase.org/db/seq/gbrowse_img/wormbase?name=B0001;add=B0001+pcr +pcr1+20000..333000;add=B0001+%22cool%20knockout%22+kn2+30000..20000,10000..500 0;type=add+CG+WTP;style=pcr+glyph=primers;style=%22cool%20knockout%22+glyph=tra nscript2+bgcolor=orange;abs=1
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 <iframe> section and using the embed=1 flag:
<iframe src=``http://localhost/cgi-bin/gbrowse_img/wormbase?name=B0001;embed=1'' width=``100%'' height=``250''> <img src=``http://localhost/cgi-bin/gbrowse_img/wormbase?name=B0001''/> </iframe>
Placing an <img> tag inside the <iframe> tag arranges for older browsers that don't know about iframes to display the static image instead. You may need to adjust the width and height attributes in order to avoid browsers placing scrollbars around the frame.
The configuration options for plugins are not correctly stored, so tracks generated by annotation plugins, such as the Restriction site annotator, will not display correctly when the image URL is generated on one machine and then viewed on another. Uploaded files will transfer correctly, however.
Lincoln Stein lstein@cshl.org
Copyright (c) 2002 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
For additional help, see The GMOD Project pages.