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Real-Time Definition of Non-Randomness in the Distribution of Genomic Events

Abel, U; Deichmann, A; Bartholomae, C; Schwarzwaelder, K; Glimm, H; Howe, S; Thrasher, A; ... Schmidt, M; + view all (2007) Real-Time Definition of Non-Randomness in the Distribution of Genomic Events. PLOS ONE , 2 (6) , Article e570. 10.1371/journal.pone.0000570. Green open access

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Abstract

Features such as mutations or structural characteristics can be non-randomly or non-uniformly distributed within a genome. So far, computer simulations were required for statistical inferences on the distribution of sequence motifs. Here, we show that these analyses are possible using an analytical, mathematical approach. For the assessment of non-randomness, our calculations only require information including genome size, number of (sampled) sequence motifs and distance parameters. We have developed computer programs evaluating our analytical formulas for the real-time determination of expected values and p-values. This approach permits a flexible cluster definition that can be applied to most effectively identify non-random or non-uniform sequence motif distribution. As an example, we show the effectivity and reliability of our mathematical approach in clinical retroviral vector integration site distribution.

Type: Article
Title: Real-Time Definition of Non-Randomness in the Distribution of Genomic Events
Open access status: An open access version is available from UCL Discovery
DOI: 10.1371/journal.pone.0000570
Publisher version: http://dx.doi.org/10.1371/journal.pone.0000570
Language: English
Additional information: © 2007 Abel et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. This work was supported by the Deutsche Forschungsgemeinschaft (Grant SPP1230), the German Ministry of Education and Research (Grant TREATID) and the EU (VIth Framework Program, CONSERT and CLINIGENE).
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health > Infection, Immunity and Inflammation Dept
URI: https://discovery.ucl.ac.uk/id/eprint/45590
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