Gaggle

The genome browser can share data with other software tools and data sources using the Gaggle integration framework.

Name lists

The genome browser can send and receive name lists. Upon receiving a name list, the browser will search for matching names in the currently loaded genome and select them.

Matrices

The genome browser can also send and receive matrices. A received matrix will be imported as a new track and plotted in the display. One subtlety is that names of rows must be mapped to coordinates on the genome. This can happen in one of several ways.

• Matching by gene names.
• Coordinates can be encoded in row names in this format: [seq][+/-]:[start]-[end]. This specifies the sequence, strand, start, and end for the feature.
• A coordinate map can be created that maps arbitrary strings (say probe IDs) to coordinates.