Epigenetic regulation consists of a multitude of different modifications that 
determine active and inactive states of chromatin. Conditions such as cell 
differentiation or exposure to environmental stress require concerted changes in 
gene expression. To interpret epigenomics data, a spectrum of different 
interconnected datasets is needed, ranging from the genome sequence and 
positions of histones, together with their modifications and variants, to the 
transcriptional output of genomic regions. Here we present a tool, Podbat 
(Positioning database and analysis tool), that incorporates data from various 
sources and allows detailed dissection of the entire range of chromatin 
modifications simultaneously. Podbat can be used to analyze, visualize, store 
and share epigenomics data. Among other functions, Podbat allows data-driven 
determination of genome regions of differential protein occupancy or RNA 
expression using Hidden Markov Models. Comparisons between datasets are 
facilitated to enable the study of the comprehensive chromatin modification 
system simultaneously, irrespective of data-generating technique. Any organism 
with a sequenced genome can be accommodated. We exemplify the power of Podbat by 
reanalyzing all to-date published genome-wide data for the histone variant H2A.Z 
in fission yeast together with other histone marks and also phenotypic response 
data from several sources. This meta-analysis led to the unexpected finding of 
H2A.Z incorporation in the coding regions of genes encoding proteins involved in 
the regulation of meiosis and genotoxic stress responses. This incorporation was 
partly independent of the H2A.Z-incorporating remodeller Swr1. We verified an 
Swr1-independent role for H2A.Z following genotoxic stress in vivo. Podbat is 
open source software freely downloadable from www.podbat.org, distributed under 
the GNU LGPL license. User manuals, test data and instructions are available at 
the website, as well as a repository for third party-developed plug-in modules. 
Podbat requires Java version 1.6 or higher.