Exploratory analysis of genomic segmentations with Segtools View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2011-10-26

AUTHORS

Orion J Buske, Michael M Hoffman, Nadia Ponts, Karine G Le Roch, William Stafford Noble

ABSTRACT

BackgroundAs 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.ResultsWe 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.ConclusionsSegtools provides a convenient, powerful means of interpreting a genomic segmentation. More... »

PAGES

415

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2105-12-415

DOI

http://dx.doi.org/10.1186/1471-2105-12-415

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1032875039

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22029426


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