Exploratory analysis of genomic segmentations with Segtools.
BACKGROUND
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.


RESULTS
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.


CONCLUSIONS
Segtools provides a convenient, powerful means of interpreting a genomic segmentation.
Department of Genome Sciences, University of Washington, PO Box 355065, Seattle, WA 98195-5065, USA.
Orion J
OJ
Buske
Michael M
MM
Hoffman
Nadia
N
Ponts
Karine G
KG
Le Roch
William Stafford
WS
Noble
D015870:Gene Expression; D015894:Genome, Human; D023281:Genomics; D042421:Histone Code; D006657:Histones / Q000378:metabolism; D006801:Humans; D010963:Plasmodium falciparum / Q000235:genetics*; D012984:Software
D006657:Histones