Plant & Animal Genomes XIII Conference Plant & Animal Genomes XIII ConferenceJanuary 15-19, 2005
Town & Country Convention Center
San Diego, CA
Xiaokang Pan1 , Lincoln Stein2 , Volker Brendel 1
We have developed SynBrowse, a synteny browser for visualizing and analyzing cross-species sequence comparisons. SynBrowse is a GBrowse family software tool developed on the basis of Bioperl modules Bio::Graphics and Bio::DB::GFF. It consists of two components: a web-based graphical interface and a set of relational databases. Each database stores pre-computed alignments between sequences of a species and its reference species as well as the gene models and other genome annotations of this species. SynBrowse has been designed to use either protein alignments or nucleotide alignments as the key comparison feature that can be complemented by other features such as gene models and other genome annotations. The graphical user-friendly interface lets end users search and browse comparisons between a query sequence and a reference sequence for syntenic blocks and then link to a set of genes (or exons), or to nucleotide alignments of a syntenic block for more detail. The tool helps scientists identify whole genome synteny, microsynteny, uncharacterized genes, putative regulatory elements and novel structural features of important species by comparing with a fully annotated reference sequence. It also assists genome curators to refine and edit annotations of the species that have immature genome annotations. Like GBrowse, SynBrowse provides system administrators with simple installation, flexible configuration, convenient data input and easy integration with other components of a model organism system. This software has been tested by sequence comparisons among genomes of dicot plant species such as Arabidopsis thaliana, Medicago truncatula, Lotus joponicus and Glycine max.