Genome-wide search for local DNA segments with anomalous GC-content. Ilatovskiy, A. & Petukhov, M. Journal of Computational Biology, 16(4):555-564, 2009. cited By 1![Genome-wide search for local DNA segments with anomalous GC-content [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex An anomalous (i.e., significantly different from genome-average) GC-content is often used as one of the markers to reveal the events of horizontal gene transfer (HGT). Unfortunately, results obtained by the traditional fixed-length window analysis strongly depend on an arbitrary selection of DNA window length. Here we present a new method for genome-wide statistical analysis of GC-content without that drawback. The method is based on a set of nonparametric statistical tests and is capable of providing reliable estimations of both a local and global GC-content, and thus can identify small local areas (as short as 30bp) with anomalous GC-content in a bacterial genome. The tests, applied to a well-studied bacterial genome of Escherichia coli K-12, show that approximately 21% of the genome belongs to the anomalous GC-content areas. Among top 23 anomalous GC-content areas, seven correspond to the annotated prophages, four to Rhs elements, and two to IS elements. A remaining 10 areas contain putative horizontally transferred DNA and genes with still unknown functions. Software is available at http://mml.spbstu.ru/gcstat. © Copyright 2009 Mary Ann Liebert, Inc.
@ARTICLE{Ilatovskiy2009555,
author={Ilatovskiy, A. and Petukhov, M.},
title={Genome-wide search for local DNA segments with anomalous GC-content},
journal={Journal of Computational Biology},
year={2009},
volume={16},
number={4},
pages={555-564},
doi={10.1089/cmb.2008.0159},
note={cited By 1},
url={https://www.scopus.com/inward/record.uri?eid=2-s2.0-64749115060&doi=10.1089%2fcmb.2008.0159&partnerID=40&md5=a81d9b2e4dcfbcb0892eec3bcf030e12},
affiliation={Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg, Russian Federation; Research and Education Centre Biophysics PNPI RAS, St. Petersburg State Polytecnic University, St. Petersburg, Russian Federation; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Orlova roscha, Gatchina /St. Petersburg, 188300, Russian Federation},
abstract={An anomalous (i.e., significantly different from genome-average) GC-content is often used as one of the markers to reveal the events of horizontal gene transfer (HGT). Unfortunately, results obtained by the traditional fixed-length window analysis strongly depend on an arbitrary selection of DNA window length. Here we present a new method for genome-wide statistical analysis of GC-content without that drawback. The method is based on a set of nonparametric statistical tests and is capable of providing reliable estimations of both a local and global GC-content, and thus can identify small local areas (as short as 30bp) with anomalous GC-content in a bacterial genome. The tests, applied to a well-studied bacterial genome of Escherichia coli K-12, show that approximately 21% of the genome belongs to the anomalous GC-content areas. Among top 23 anomalous GC-content areas, seven correspond to the annotated prophages, four to Rhs elements, and two to IS elements. A remaining 10 areas contain putative horizontally transferred DNA and genes with still unknown functions. Software is available at http://mml.spbstu.ru/gcstat. © Copyright 2009 Mary Ann Liebert, Inc.},
author_keywords={GC-content; Genome; Horizontal gene transfer; Sequence analysis},
correspondence_address1={Ilatovskiy, A.; Division of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, Russian Academy of Sciences, Gatchina/St. Petersburg, Russian Federation; email: andreyi@omrb.pnpi.spb.ru},
issn={10665277},
coden={JCOBE},
pubmed_id={19361327},
language={English},
abbrev_source_title={J. Comput. Biol.},
document_type={Article},
source={Scopus},
}
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