The availability of genome wide functional data is one of the major changes in genomics in the last few years. Driven by involvement in analysis for the ENCODE project (9) and other international research consortia such as the EU FP6 funded HEROIC (High-throughput Epigenetic Regulatory Organisation In Chromatin) project, Ensembl has built up an infrastructure to support handling and display of this class of data (14). We have also recently participated in the creation of a genome-wide DNA methylation resource that has been incorporated into Ensembl (33,34). With the availability of next generation sequencing technology, array based ChIP-chip functional data is very rapidly giving way to sequence based ChIP-seq data. A major activity this year has been the development of a ChIP-seq analysis pipeline including a custom algorithm for the analysis of ChIP-seq data.
