{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T14:48:10Z","timestamp":1780411690453,"version":"3.54.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"16","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,8,15]]},"abstract":"<jats:p>Motivation: DNA segmentation, i.e. the partitioning of DNA in compositionally homogeneous segments, is a basic task in bioinformatics. Different algorithms have been proposed for various partitioning criteria such as Guanine\/Cytosine (GC) content, local ancestry in population genetics or copy number variation. A critical component of any such method is the choice of an appropriate number of segments. Some methods use model selection criteria and do not provide a suitable error control. Other methods that are based on simulating a statistic under a null model provide suitable error control only if the correct null model is chosen.<\/jats:p>\n               <jats:p>Results: Here, we focus on partitioning with respect to GC content and propose a new approach that provides statistical error control: as in statistical hypothesis testing, it guarantees with a user-specified probability that the number of identified segments does not exceed the number of actually present segments. The method is based on a statistical multiscale criterion, rendering this as a segmentation method that searches segments of any length (on all scales) simultaneously. It is also accurate in localizing segments: under benchmark scenarios, our approach leads to a segmentation that is more accurate than the approaches discussed in the comparative review of Elhaik et al. In our real data examples, we find segments that often correspond well to features taken from standard University of California at Santa Cruz (UCSC) genome annotation tracks.<\/jats:p>\n               <jats:p>Availability and implementation: Our method is implemented in function smuceR of the R-package stepR available at http:\/\/www.stochastik.math.uni-goettingen.de\/smuce.<\/jats:p>\n               <jats:p>Contact: \u00a0andreas.futschik@jku.at or thomas.hotz@tu-ilmenau.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu180","type":"journal-article","created":{"date-parts":[[2014,4,22]],"date-time":"2014-04-22T00:28:11Z","timestamp":1398126491000},"page":"2255-2262","source":"Crossref","is-referenced-by-count":19,"title":["Multiscale DNA partitioning: statistical evidence for segments"],"prefix":"10.1093","volume":"30","author":[{"given":"Andreas","family":"Futschik","sequence":"first","affiliation":[{"name":"1 \u00a01Department of Applied Statistics, JK University Linz, A-4040 Linz, Austria, 2Institute of Mathematics, Technische Universit\u00e4t Ilmenau, D-98693 Ilmenau, Germany, 3Institute for Mathematical Stochastics and Felix Bernstein Institute for Mathematical Statistics in Biosciences, Georgia Augusta University of Goettingen and 4Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Hotz","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Applied Statistics, JK University Linz, A-4040 Linz, Austria, 2Institute of Mathematics, Technische Universit\u00e4t Ilmenau, D-98693 Ilmenau, Germany, 3Institute for Mathematical Stochastics and Felix Bernstein Institute for Mathematical Statistics in Biosciences, Georgia Augusta University of Goettingen and 4Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Axel","family":"Munk","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Applied Statistics, JK University Linz, A-4040 Linz, Austria, 2Institute of Mathematics, Technische Universit\u00e4t Ilmenau, D-98693 Ilmenau, Germany, 3Institute for Mathematical Stochastics and Felix Bernstein Institute for Mathematical Statistics in Biosciences, Georgia Augusta University of Goettingen and 4Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannes","family":"Sieling","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Applied Statistics, JK University Linz, A-4040 Linz, Austria, 2Institute of Mathematics, Technische Universit\u00e4t Ilmenau, D-98693 Ilmenau, Germany, 3Institute for Mathematical Stochastics and Felix Bernstein Institute for Mathematical Statistics in Biosciences, Georgia Augusta University of Goettingen and 4Max Planck Institute for Biophysical Chemistry, D-37077 Goettingen, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,4,21]]},"reference":[{"key":"2023012711523485100_btu180-B1","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1016\/j.celrep.2012.03.013","article-title":"Differential GC content between exons and introns establishes distinct strategies of splice-site recognition","volume":"1","author":"Amit","year":"2012","journal-title":"Cell Rep."},{"key":"2023012711523485100_btu180-B2","doi-asserted-by":"crossref","first-page":"e72","DOI":"10.1093\/nar\/gks001","article-title":"Summarizing and correcting the GC content bias in high-throughput sequencing","volume":"40","author":"Benjamini","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2023012711523485100_btu180-B5","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0378-1119(01)00644-8","article-title":"Misunderstandings about isochores. Part I","volume":"276","author":"Bernardi","year":"2001","journal-title":"Gene"},{"key":"2023012711523485100_btu180-B6","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1214\/07-AOS558","article-title":"Consistencies and rates of convergence of jump-penalized least squares estimators","volume":"37","author":"Boysen","year":"2009","journal-title":"Ann. Statist."},{"key":"2023012711523485100_btu180-B7","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1214\/ss\/1028905933","article-title":"Statistical methods for DNA segmentation","volume":"13","author":"Braun","year":"1998","journal-title":"Stat. Sci."},{"key":"2023012711523485100_btu180-B8","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1093\/biomet\/87.2.301","article-title":"Multiple change-point fitting via quasi-likelihood, with application to DNA sequence segmentation","volume":"87","author":"Braun","year":"2000","journal-title":"Biometrika"},{"key":"2023012711523485100_btu180-B9","volume-title":"Computational Genomics","author":"Cristianini","year":"2007"},{"key":"2023012711523485100_btu180-B10","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/S0092-8240(89)80049-7","article-title":"Stochastic models for heterogeneous DNA sequences","volume":"51","author":"Churchill","year":"1989","journal-title":"Bull. Math. Biol."},{"key":"2023012711523485100_btu180-B11","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/0097-8485(92)80037-Z","article-title":"Hidden Markov chains and the analysis of genome structure","volume":"16","author":"Churchill","year":"1992","journal-title":"Comp. Chem."},{"key":"2023012711523485100_btu180-B12","doi-asserted-by":"crossref","first-page":"1524","DOI":"10.1016\/S0378-1119(01)00667-9","article-title":"Compositional heterogeneity within and among isochores in mammalian genomes. I. CsCl and sequence analyses","volume":"276","author":"Clay","year":"2001","journal-title":"Gene"},{"key":"2023012711523485100_btu180-B13","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1093\/molbev\/msi115","article-title":"GC composition of the human genome: in search for isochores","volume":"22","author":"Cohen","year":"2005","journal-title":"Mol. Biol. Evol."},{"key":"2023012711523485100_btu180-B15","doi-asserted-by":"crossref","first-page":"3623","DOI":"10.1016\/j.csda.2010.06.027","article-title":"Recursive computation of piecewise constant volatilities","volume":"11","author":"Davies","year":"2012","journal-title":"Comput. Stat. Data Anal."},{"key":"2023012711523485100_btu180-B16","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1214\/aos\/996986504","article-title":"Multiscale testing of qualitative hypotheses","volume":"29","author":"D\u00fcmbgen","year":"2001","journal-title":"Ann. Stat."},{"key":"2023012711523485100_btu180-B17","doi-asserted-by":"crossref","first-page":"1758","DOI":"10.1214\/07-AOS521","article-title":"Multiscale inference about a density","volume":"36","author":"D\u00fcmbgen","year":"2008","journal-title":"Ann. Stat."},{"key":"2023012711523485100_btu180-B18","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1093\/molbev\/msp307","article-title":"Comparative testing of DNA segmentation algorithms using benchmark simulations","volume":"27","author":"Elhaik","year":"2010","journal-title":"Mol. Biol. Evol."},{"key":"2023012711523485100_btu180-B19","doi-asserted-by":"crossref","first-page":"e158","DOI":"10.1093\/nar\/gkq532","article-title":"Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm","volume":"38","author":"Elhaik","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012711523485100_btu180-B20","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1016\/0888-7543(92)90019-O","article-title":"Base compositional structure of genomes","volume":"13","author":"Fickett","year":"1992","journal-title":"Genomics"},{"key":"2023012711523485100_btu180-B21","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1111\/rssb.12047","article-title":"Multiscale change-point inference","volume":"76","author":"Frick","year":"2014","journal-title":"J. R. Stat. Soc. Ser."},{"key":"2023012711523485100_btu180-B22","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1198\/106186008X285591","article-title":"Complexity penalized M- estimation: fast computation","volume":"17","author":"Friedrich","year":"2008","journal-title":"J. Comput. Graph. Stat."},{"key":"2023012711523485100_btu180-B23","doi-asserted-by":"crossref","first-page":"S66","DOI":"10.1186\/1471-2105-10-S1-S66","article-title":"Partial correlation analysis indicates causal relationships between GC-content, exon density and recombination rate in the human genome","volume":"10","author":"Freudenberg","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012711523485100_btu180-B24","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1093\/oxfordjournals.molbev.a003886","article-title":"Local rates of recombination are positively correlated with GC content in the human genome","volume":"18","author":"Fullerton","year":"2001","journal-title":"Mol. Biol. Evol."},{"key":"2023012711523485100_btu180-B25","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1093\/genetics\/159.2.907","article-title":"GC-content evolution in mammalian genomes: the biased gene conversion hypothesis","volume":"159","author":"Galtier","year":"2001","journal-title":"Genetics"},{"key":"2023012711523485100_btu180-B26","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1089\/cmb.2006.13.1369","article-title":"Segmenting eukaryotic genomes with the generalized gibbs sampler","volume":"13","author":"Keith","year":"2006","journal-title":"J. Comput. Biol."},{"key":"2023012711523485100_btu180-B27","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1080\/01621459.2012.737745","article-title":"Optimal detection of changepoints with a linear computational cost","volume":"107","author":"Killick","year":"2012","journal-title":"J. Am. Stat. Assoc."},{"key":"2023012711523485100_btu180-B28","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1093\/bioinformatics\/15.12.974","article-title":"SEGMENT: identifying compositional domains in DNA sequences","volume":"15","author":"Oliver","year":"1999","journal-title":"Bioinformatics"},{"key":"2023012711523485100_btu180-B29","doi-asserted-by":"crossref","first-page":"480","DOI":"10.1186\/1471-2105-12-480","article-title":"GC-Content Normalization for RNA-Seq Data","volume":"12","author":"Risso","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023012711523485100_btu180-B30","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1073\/pnas.48.4.582","article-title":"On the genetic basis of variation and heterogeneity of DNA base composition","volume":"48","author":"Sueoka","year":"1962","journal-title":"PNAS"},{"key":"2023012711523485100_btu180-B31","doi-asserted-by":"crossref","first-page":"1010","DOI":"10.1214\/09-AOS732","article-title":"Optimal and fast detection of spatial clusters with scan statistics","volume":"38","author":"Walther","year":"2010","journal-title":"Ann. Statist."},{"key":"2023012711523485100_btu180-B32","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1080\/10485250211388","article-title":"Smoothers for discontinuous signals","volume":"14","author":"Winkler","year":"2002","journal-title":"J. Nonparametr. Stat."},{"key":"2023012711523485100_btu180-B34","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/0167-7152(88)90118-6","article-title":"Estimating the number of change-points via Schwarz\u2019 criterion","volume":"6","author":"Yao","year":"1988","journal-title":"Statist. Probab. Lett."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/16\/2255\/48926348\/bioinformatics_30_16_2255.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/16\/2255\/48926348\/bioinformatics_30_16_2255.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:14:03Z","timestamp":1674821643000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/16\/2255\/2748136"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,4,21]]},"references-count":30,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2014,8,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu180","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,4,21]]}}}