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ArchAlign: coordinate-free chromatin alignment reveals novel architectures

William KM Lai and Michael J Buck*

Author Affiliations

Department of Biochemistry and the Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, 701 Ellicott St, Buffalo, New York 14203, USA

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Genome Biology 2010, 11:R126  doi:10.1186/gb-2010-11-12-r126

Published: 23 December 2010

Abstract

To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets derived from next-generation sequencing or tiled microarray approaches for user defined regions of interest. We validated ArchAlign using well characterized functional elements, and used it to explore the chromatin structural architecture at CTCF binding sites in the human genome. ArchAlign is freely available at http://www.acsu.buffalo.edu/~mjbuck/ArchAlign.html webcite.