SyMAP: Dynamic Synteny Exploration

SyMAP v3.5 is a self-contained software package for synteny analysis and display. The inputs can be either sequenced chromosomes, draft sequenced contigs, or a BAC fingerprint map, along with annotation. The software calls MUMmer or BLAT to compute alignment anchors between each species pair, filters repetitive anchors using a reciprocal top-N filter, and then applies a heuristic algorithm which scans over a wide space of gap parameters to detect synteny blocks. Both primary and duplicated blocks are found. A variety of interfaces are provided to explore the results including:  dynamic 3D and circular views, in which chromosomes from different species may be added to the view or removed as desired; a multi-species/multi-chromosome dot plot view; and a zoomable side-by-side view, which shows the annotation and allows detailed exploration down to the level of individual basepairs.  The software, and a showcase focusing on plant genomes, is available at http://www.symapdb.org.