Interacting with other genome browsers & Track lines

Interacting with other genome browsers

IGB can be used in conjunction with other applications, including web-based genome browsers.  Web-based browsers have the advantages of being installed and maintained on a remote computer, and of giving you access to large amounts of remotely-stored data.  IGB, and other stand-alone applications, have the advantages of more rapid navigation, ability to work when off-line, and secure access to private, local data.  It is thus natural that users will make use of web-based applications along with IGB.

Web-based browsers include

• Ø The UCSC Genome Browser

[http://genome.ucsc.edu/|http://genome.ucsc.edu/]
* Ø GBrowse, from the Generic Model Organism Database project

[http://www.gmod.org/|http://www.gmod.org/]

By using some of the standardized data file formats, such as FASTA for sequences, data files can be used in multiple applications. 

IGB contains a menu item that will open the UCSC browser on the same region you are currently viewing.  IGB also allows the configuration of selection-based links to other web-pages.

The reverse process is also possible.  Web pages and other programs can control IGB through the use of hyperlinks.  See the section Controlling IGB through a browser below.

To facilitate sharing of data files between IGB and the UCSC browser, IGB allows the use of track lines to specify some display properties.  Since these track lines were defined by UCSC for use in their browser, not all properties are directly applicable in IGB, but those which are applicable are used.  See

[http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK|http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK]


h2. *[Track lines|#tracklines]*

For many text-based file formats, it is possible to configure the track name,  color, and other properties through the use of track lines in the file header or comments.  Track lines were invented for use in the UCSC genome browser, and the full format is described on their web site.  IGB understands a subset of the full format, and will ignore property settings that it doesn't use.

In ".wig", ".bed", ".psl", or "gff" format (version 1 or 2), the track line begins with "track".  In ".gff" format version 3, the track line must begin with "##track" to indicate it as a meta-directive, since track lines would otherwise disobey the GFF3 specification.  (GFF3 has its own rich methods of specifying annotation styles.  A future version of IGB may make use of this.)

Here is a sample track line that can be understood by IGB:

track name="Example" description="Example Description" visibility=full color=200,100,0 useScore=1 url="*[http://sample.com/search?id=$$|http://sample.com/search?id=$$]*"

IGB understands these track line properties: