<img src="http://www.wormbase.org/db/seq/gbrowse_img/elegans?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 fly yeast wormbase<a href="http://www.wormbase.org/db/seq/gbrowse_img/elegans?list=types">types</a>Will return this document: ## Feature types for source wormbase tRNA tRNAs NG Named Genes default CG Curated genes default PG Predicted genes WABA Briggsae alignments (WABA) ESTB ESTs aligned by BLAT (best) ESTO ESTs aligned by BLAT (other) mRNAB mRNAs aligned by BLAT (best) mRNAO mRNAs aligned by BLAT (other) RNAi RNAi experiments EXPR Expression chip profiles WTP Worm Transcriptome Project genes SNP SNPs TcI Transposon Insertions
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:
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. Many of the options have one-letter aliases that can be used to reduce URL lengths.
|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|
|grid||turn grid on (1) or off (0)|
|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|
The arguments are explained in more detail here
<img src="http://www.wormbase.org/db/seq/gbrowse_img/elegans?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:
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:
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.
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.
h_feat=SKT5@blueYou may omit "@color", in which case the highlight will default to yellow. You can specify multiple h_feat arguments in order to highlight several features with distinct colors.
h_region=Chr3:200000..250000@wheatYou may omit "@color", in which case the highlighted region will default to lightgrey. You can specify multiple h_region arguments in order to highlight several regions with distinct colors.
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 <iframe> section and using the embed=1 flag:
<iframe src="http://localhost/cgi-bin/gbrowse_img/elegans?name=B0001;embed=1" width="100%" height="250"> <img src="http://localhost/cgi-bin/gbrowse_img/elegans?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 cookie that stores the configuration options for plugins does not transfer from gbrowse to gbrowse_img, 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 email@example.com
Copyright (c) 2002-2004 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.