Developing draft genomes are often fragmented and multi-layered frameworks. Visualizing these complex infrastructures requires the integration of large volumes of diverse information/data from disparate sources. Existing genome browsers are not well adapted to this task as they expect all genomic features to be anchored to a single linearly ordered reference sequence. We developed the barley genome explorer BARLEX, as a central unified repository for the genomic resources of barley (Hordeum vulgare L.). BARLEX is centered on the genome-wide physical map of barley and links it to an annotated whole-genome shotgun assembly and dense genetic maps. A web-based interface presents data in tabular and graphical format and associates all information and published sequence data with shotgun assemblies, physical contigs and annotated genes. A novel graph-based visualization strategy was implemented to show overlaps between adjacent BACs based on fingerprint and sequence data. BARLEX is publicly accessible at http://barlex.barleysequence.org.