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Exploratory analysis of genomic segmentations with Segtools

Orion J Buske1, Michael M Hoffman1, Nadia Ponts2, Karine G Le Roch2 and William Stafford Noble13*

Author Affiliations

1 Department of Genome Sciences, University of Washington, PO Box 355065, Seattle, WA 98195-5065, USA

2 The Institute for Integrative Genome Biology, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA

3 Department of Computer Science and Engineering, University of Washington, PO Box 352350, Seattle, WA 98195-2350, USA

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BMC Bioinformatics 2011, 12:415  doi:10.1186/1471-2105-12-415

Published: 26 October 2011



As genome-wide experiments and annotations become more prevalent, researchers increasingly require tools to help interpret data at this scale. Many functional genomics experiments involve partitioning the genome into labeled segments, such that segments sharing the same label exhibit one or more biochemical or functional traits. For example, a collection of ChlP-seq experiments yields a compendium of peaks, each labeled with one or more associated DNA-binding proteins. Similarly, manually or automatically generated annotations of functional genomic elements, including cis-regulatory modules and protein-coding or RNA genes, can also be summarized as genomic segmentations.


We present a software toolkit called Segtools that simplifies and automates the exploration of genomic segmentations. The software operates as a series of interacting tools, each of which provides one mode of summarization. These various tools can be pipelined and summarized in a single HTML page. We describe the Segtools toolkit and demonstrate its use in interpreting a collection of human histone modification data sets and Plasmodium falciparum local chromatin structure data sets.


Segtools provides a convenient, powerful means of interpreting a genomic segmentation.