Visualization of syntenic relationships with SynBrowse.

Synteny is the preserved order of genes between related species. To detect syntenic regions one usually first applies sequence comparison methods to the genomic sequences of the considered species. Sequence similarities detected in this way often require manual curation to finally reveal the-in many cases-hidden syntenies. The open source software SynBrowse provides a convenient interface to visualize syntenies on a genomic scale. SynBrowse is based on the well-known GBrowse software. In this chapter, we describe the basic concepts of SynBrowse and show how to apply it to different kinds of data sets. Our exposition includes the description of software pipelines for the complete process of synteny detection: (1) applying standard software to compute sequence similarities, (2) parsing, combining, and storing detected similarities in a standard database, (3) installing, configuring, and using SynBrowse. The complete set of programs making up these pipelines as well as the data sets used are available on the SynBrowse homepage.