BACKGROUND: Chromatin immunoprecipitation (ChIP) followed by high-throughput 
sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis 
(ChIP-chip) have become standard technologies for genome-wide identification of 
DNA-binding protein target sites. A number of algorithms have been developed in 
parallel that allow identification of binding sites from ChIP-seq or ChIP-chip 
datasets and subsequent visualization in the University of California Santa Cruz 
(UCSC) Genome Browser as custom annotation tracks. However, summarizing these 
tracks can be a daunting task, particularly if there are a large number of 
binding sites or the binding sites are distributed widely across the genome.
RESULTS: We have developed ChIPpeakAnno as a Bioconductor package within the 
statistical programming environment R to facilitate batch annotation of enriched 
peaks identified from ChIP-seq, ChIP-chip, cap analysis of gene expression 
(CAGE) or any experiments resulting in a large number of enriched genomic 
regions. The binding sites annotated with ChIPpeakAnno can be viewed easily as a 
table, a pie chart or plotted in histogram form, i.e., the distribution of 
distances to the nearest genes for each set of peaks. In addition, we have 
implemented functionalities for determining the significance of overlap between 
replicates or binding sites among transcription factors within a complex, and 
for drawing Venn diagrams to visualize the extent of the overlap between 
replicates. Furthermore, the package includes functionalities to retrieve 
sequences flanking putative binding sites for PCR amplification, cloning, or 
motif discovery, and to identify Gene Ontology (GO) terms associated with 
adjacent genes.
CONCLUSIONS: ChIPpeakAnno enables batch annotation of the binding sites 
identified from ChIP-seq, ChIP-chip, CAGE or any technology that results in a 
large number of enriched genomic regions within the statistical programming 
environment R. Allowing users to pass their own annotation data such as a 
different Chromatin immunoprecipitation (ChIP) preparation and a dataset from 
literature, or existing annotation packages, such as GenomicFeatures and 
BSgenome, provides flexibility. Tight integration to the biomaRt package enables 
up-to-date annotation retrieval from the BioMart database.