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Exploratory analysis of genomic segmentations with Segtools

Orion J Buske, Michael M Hoffman, Nadia Ponts, Karine G Le Roch, William Noble
2011 BMC Bioinformatics  
Results: We present a software toolkit called Segtools that simplifies and automates the exploration of genomic segmentations.  ...  Conclusions: Segtools provides a convenient, powerful means of interpreting a genomic segmentation. Authors' contributions MMH and WSN conceived of and supervised the project.  ...  This work was funded by the National Institutes of Health [HG004695].  ... 
doi:10.1186/1471-2105-12-415 pmid:22029426 pmcid:PMC3224787 fatcat:gqrklxk3pjehbkstevk4brl7li

Semi-automated genome annotation using epigenomic data and Segway [article]

Eric G. Roberts, Mickaël Mendez, Coby Viner, Mehran Karimzadeh, Rachel C. W. Chan, Rachel Ancar, Davide Chicco, Jay R. Hesselberth, Anshul Kundaje, Michael M. Hoffman
2016 bioRxiv   pre-print
This protocol describes how to use Segway to annotate the genome, starting with reads from a ChIP-seq experiment.  ...  Biochemical techniques measure many individual properties of chromatin along the genome.  ...  Segtools 33 (segtools.hoffmanlab.org) is a collection of command-line tools that enables exploratory data analysis of genome segmentations, such as the output of Segway.  ... 
doi:10.1101/080382 fatcat:ztqkrl32arbzveicwcxvoad2oq

PREDICTION OF CHROMATIN STATES USING DNA SEQUENCE PROPERTIES

Rihab Riyad Bahabri
2013 unpublished
Buske and Hoffman et al. [45] developed a tool for exploratory analysis of genomic segmentations.  ...  They introduced a command-line tool "HMMSeg" for unsupervised segmentation of the genome.  ... 
fatcat:c3koqjfwc5gwlhsszcawpjiwi4

Computational studies in epigenomics using histone modification data

Nishanth Ulhas Nair
2014
With immense gratitude I thank Amma and Achhan for all that they have done for me and for being my parents. My brother Nitin has always been my well-wisher.  ...  Sriram Sankararaman has been a constant source of inspiration for me, and it was partly because of him that I chose to pick computational biology as my area of research.  ...  The short segments of DNA are treated with a specific antibody to capture a particular histone modification in the genome. The rest of the fragments are washed away.  ... 
doi:10.5075/epfl-thesis-6327 fatcat:tzvav22vyzffbchxl22s5q4kv4