GMOD Resources

Demos

Links to Related Projects

GMOD is supported by a specific cooperative agreement from the USDA Agricultural Research Service, and by NIH grants co-funded from the National Human Genome Research Institute and the National Institute of General Medical Sciences.

gbrowse_img - CGI script to generate genome images via the Generic Genome Browser
SYNOPSIS
DESCRIPTION
CGI arguments
AUTHOR

gbrowse_img - CGI script to generate genome images via the Generic Genome Browser

SYNOPSIS

  <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

DESCRIPTION

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.

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                  Description
   list     get certain types of configuration information
   source   database name
   name     genomic landmark or range
   type     list of feature names
   width    desired width of image
   options  list of track options (compact, labeled, etc)
   add      additional features to superimpose on image
   abs      display position in absolute coordinates

The arguments are explained in more detail here

list

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 follows:

   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.

source

This argument specifies the database for the images. The list of sources can be found using list=sources.

name

This argument specifies the region of the genome to be displayed. Several forms are recognized:

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.

type

This argument lists the feature types to display. The value of this argument is a list of mnemonics separated by spaces (``+'' characters when URL-escaped). For example:


  <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.

options

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:

   options=tRNA+3+NG+3+WABA+1

add

Superimpose one or more additional features on top of the view. Features are specified as space (``+'') delimited lists in the following format:

   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

Multiple add= arguments are allowed.

abs

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 default).

AUTHOR

Lincoln Stein lstein@cshl.org

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.

Gramene: A Comparative Mapping Resource for Grains

cain@cshl.org