id:"swepub:oai:gup.ub.gu.se/285816"
Search: id:"swepub:oai:gup.ub.gu.se/285816" > Bayesian localizati...
- 1 of 1
- Previous record
- Next record
- To hitlist
Bayesian localization of CNV candidates in WGS data within minutes
-
- Wiedenhoeft, John, 1982 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för data- och informationsteknik, datavetenskap (GU),Department of Computer Science and Engineering, Computing Science (GU),Chalmers tekniska högskola,Chalmers University of Technology,Rutgers University
-
- Cagan, A. (author)
- Wellcome Trust Sanger Institute,Max Planck Gesellschaft zur Förderung der Wissenschaften e.V. (MPG),Max Planck Society for the Advancement of Science (MPG)
-
- Kozhemyakina, R. (author)
- Russian Academy of Sciences
- show more...
- show less...
- (creator_code:org_t)
- 2019-09-23
- 2019
- English.
- In: Algorithms for Molecular Biology. - : Springer Science and Business Media LLC. - 1748-7188. ; 14:1
- Journal article (peer-reviewed)
Abstract
Subject headings
Close
- Background Full Bayesian inference for detecting copy number variants (CNV) from whole-genome sequencing (WGS) data is still largely infeasible due to computational demands. A recently introduced approach to perform Forward-Backward Gibbs sampling using dynamic Haar wavelet compression has alleviated issues of convergence and, to some extent, speed. Yet, the problem remains challenging in practice. Results In this paper, we propose an improved algorithmic framework for this approach. We provide new space-efficient data structures to query sufficient statistics in logarithmic time, based on a linear-time, in-place transform of the data, which also improves on the compression ratio. We also propose a new approach to efficiently store and update marginal state counts obtained from the Gibbs sampler. Conclusions Using this approach, we discover several CNV candidates in two rat populations divergently selected for tame and aggressive behavior, consistent with earlier results concerning the domestication syndrome as well as experimental observations. Computationally, we observe a 29.5-fold decrease in memory, an average 5.8-fold speedup, as well as a 191-fold decrease in minor page faults. We also observe that metrics varied greatly in the old implementation, but not the new one. We conjecture that this is due to the better compression scheme. The fully Bayesian segmentation of the entire WGS data set required 3.5 min and 1.24 GB of memory, and can hence be performed on a commodity laptop.
Subject headings
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- NATURVETENSKAP -- Matematik -- Sannolikhetsteori och statistik (hsv//swe)
- NATURAL SCIENCES -- Mathematics -- Probability Theory and Statistics (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Datorseende och robotik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Computer Vision and Robotics (hsv//eng)
Keyword
- HMM
- Wavelet
- CNV
- Bayesian inference
- hidden markov-models
- analysis toolkit
- domestication
- adaptation
- webgestalt
- evolution
- variants
- behavior
- fox
- Biochemistry & Molecular Biology
- Biotechnology & Applied Microbiology
- Mathematical & Computational Biology
- HMM
Publication and Content Type
- ref (subject category)
- art (subject category)
Find in a library
- Algorithms for Molecular Biology (Search for host publication in LIBRIS)
To the university's database
- 1 of 1
- Previous record
- Next record
- To hitlist
Find more in SwePub
- By the author/editor
- Wiedenhoeft, Joh ...
- Cagan, A.
- Kozhemyakina, R.
- Gulevich, R.
- Schliep, Alexand ...
- About the subject
-
- NATURAL SCIENCES
- NATURAL SCIENCES
- and Biological Scien ...
- and Biochemistry and ...
-
- NATURAL SCIENCES
- NATURAL SCIENCES
- and Computer and Inf ...
- and Bioinformatics
-
- NATURAL SCIENCES
- NATURAL SCIENCES
- and Mathematics
- and Probability Theo ...
-
- NATURAL SCIENCES
- NATURAL SCIENCES
- and Computer and Inf ...
- and Computer Vision ...
- Articles in the publication
- Algorithms for M ...
- By the university
- University of Gothenburg
- Chalmers University of Technology
Search outside SwePub
- Extend your search to:
- Google Book Search
- Google Scholar
Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.
- Copyright © LIBRIS - National Library Systems
- LIBRIS.kb.se
