Regions of unusual statistical properties as tools in the search for horizontally transferred genes in Escherichia coli

Catherine Putonti, Sergei Chumakov, Arturo Chavez, Yi Luo, Dan Graur, George E. Fox, Yuriy Fofanov

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The observed diversity of statistical characteristics along genomic sequences is the result of the influences of a variety of ongoing processes including horizontal gene transfer, gene loss, genome rearrangements, and evolution. The rate at which various processes affect the genome typically varies between different genomic regions. Thus, variations in statistical properties seen in different regions of a genome are often associated with its evolution and functional organization. Analysis of such properties is therefore relevant to many ongoing biomedical research efforts. Similarity Plot or S-plot is a Windows-based application for large-scale comparisons and 2D visualization of similarities between genomic sequences. This application combines two approaches wildly used in genomics: window analysis of statistical characteristics along genomes and dot-plot visual representation. S-plot is effective in detecting highly similar regions between two genomes. Within a single genome, S-plot has the ability to identify highly dissimilar regions displaying unusual compositional properties. The application was used to perform a comparative analysis of 50+ microbial genomes as well as many eukaryote genomes including human, rat, mouse, and drosophila. We illustrate the uses of S-Plot in a comparison involving Escherichia coli K12 and E. coli O157:H7.

Original languageEnglish (US)
Title of host publicationAIP Conference Proceedings
Pages126-128
Number of pages3
Volume854
DOIs
StatePublished - 2006
Externally publishedYes
Event9h Mexican Symposium on Medical Physics - Guadalajara, Jalisco, Mexico
Duration: Mar 18 2006Mar 23 2006

Other

Other9h Mexican Symposium on Medical Physics
CountryMexico
CityGuadalajara, Jalisco
Period3/18/063/23/06

Fingerprint

genome
Escherichia
genes
plots
eukaryotes
Drosophila
rats
mice

Keywords

  • Escherichia coli K12
  • Escherichia coli O157:H7
  • Horizontal gene transfer
  • Sequence composition

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Cite this

Putonti, C., Chumakov, S., Chavez, A., Luo, Y., Graur, D., Fox, G. E., & Fofanov, Y. (2006). Regions of unusual statistical properties as tools in the search for horizontally transferred genes in Escherichia coli. In AIP Conference Proceedings (Vol. 854, pp. 126-128) https://doi.org/10.1063/1.2356423

Regions of unusual statistical properties as tools in the search for horizontally transferred genes in Escherichia coli. / Putonti, Catherine; Chumakov, Sergei; Chavez, Arturo; Luo, Yi; Graur, Dan; Fox, George E.; Fofanov, Yuriy.

AIP Conference Proceedings. Vol. 854 2006. p. 126-128.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Putonti, C, Chumakov, S, Chavez, A, Luo, Y, Graur, D, Fox, GE & Fofanov, Y 2006, Regions of unusual statistical properties as tools in the search for horizontally transferred genes in Escherichia coli. in AIP Conference Proceedings. vol. 854, pp. 126-128, 9h Mexican Symposium on Medical Physics, Guadalajara, Jalisco, Mexico, 3/18/06. https://doi.org/10.1063/1.2356423
Putonti C, Chumakov S, Chavez A, Luo Y, Graur D, Fox GE et al. Regions of unusual statistical properties as tools in the search for horizontally transferred genes in Escherichia coli. In AIP Conference Proceedings. Vol. 854. 2006. p. 126-128 https://doi.org/10.1063/1.2356423
Putonti, Catherine ; Chumakov, Sergei ; Chavez, Arturo ; Luo, Yi ; Graur, Dan ; Fox, George E. ; Fofanov, Yuriy. / Regions of unusual statistical properties as tools in the search for horizontally transferred genes in Escherichia coli. AIP Conference Proceedings. Vol. 854 2006. pp. 126-128
@inproceedings{0fe5b1579e2f401583ebad60d93d9084,
title = "Regions of unusual statistical properties as tools in the search for horizontally transferred genes in Escherichia coli",
abstract = "The observed diversity of statistical characteristics along genomic sequences is the result of the influences of a variety of ongoing processes including horizontal gene transfer, gene loss, genome rearrangements, and evolution. The rate at which various processes affect the genome typically varies between different genomic regions. Thus, variations in statistical properties seen in different regions of a genome are often associated with its evolution and functional organization. Analysis of such properties is therefore relevant to many ongoing biomedical research efforts. Similarity Plot or S-plot is a Windows-based application for large-scale comparisons and 2D visualization of similarities between genomic sequences. This application combines two approaches wildly used in genomics: window analysis of statistical characteristics along genomes and dot-plot visual representation. S-plot is effective in detecting highly similar regions between two genomes. Within a single genome, S-plot has the ability to identify highly dissimilar regions displaying unusual compositional properties. The application was used to perform a comparative analysis of 50+ microbial genomes as well as many eukaryote genomes including human, rat, mouse, and drosophila. We illustrate the uses of S-Plot in a comparison involving Escherichia coli K12 and E. coli O157:H7.",
keywords = "Escherichia coli K12, Escherichia coli O157:H7, Horizontal gene transfer, Sequence composition",
author = "Catherine Putonti and Sergei Chumakov and Arturo Chavez and Yi Luo and Dan Graur and Fox, {George E.} and Yuriy Fofanov",
year = "2006",
doi = "10.1063/1.2356423",
language = "English (US)",
volume = "854",
pages = "126--128",
booktitle = "AIP Conference Proceedings",

}

TY - GEN

T1 - Regions of unusual statistical properties as tools in the search for horizontally transferred genes in Escherichia coli

AU - Putonti, Catherine

AU - Chumakov, Sergei

AU - Chavez, Arturo

AU - Luo, Yi

AU - Graur, Dan

AU - Fox, George E.

AU - Fofanov, Yuriy

PY - 2006

Y1 - 2006

N2 - The observed diversity of statistical characteristics along genomic sequences is the result of the influences of a variety of ongoing processes including horizontal gene transfer, gene loss, genome rearrangements, and evolution. The rate at which various processes affect the genome typically varies between different genomic regions. Thus, variations in statistical properties seen in different regions of a genome are often associated with its evolution and functional organization. Analysis of such properties is therefore relevant to many ongoing biomedical research efforts. Similarity Plot or S-plot is a Windows-based application for large-scale comparisons and 2D visualization of similarities between genomic sequences. This application combines two approaches wildly used in genomics: window analysis of statistical characteristics along genomes and dot-plot visual representation. S-plot is effective in detecting highly similar regions between two genomes. Within a single genome, S-plot has the ability to identify highly dissimilar regions displaying unusual compositional properties. The application was used to perform a comparative analysis of 50+ microbial genomes as well as many eukaryote genomes including human, rat, mouse, and drosophila. We illustrate the uses of S-Plot in a comparison involving Escherichia coli K12 and E. coli O157:H7.

AB - The observed diversity of statistical characteristics along genomic sequences is the result of the influences of a variety of ongoing processes including horizontal gene transfer, gene loss, genome rearrangements, and evolution. The rate at which various processes affect the genome typically varies between different genomic regions. Thus, variations in statistical properties seen in different regions of a genome are often associated with its evolution and functional organization. Analysis of such properties is therefore relevant to many ongoing biomedical research efforts. Similarity Plot or S-plot is a Windows-based application for large-scale comparisons and 2D visualization of similarities between genomic sequences. This application combines two approaches wildly used in genomics: window analysis of statistical characteristics along genomes and dot-plot visual representation. S-plot is effective in detecting highly similar regions between two genomes. Within a single genome, S-plot has the ability to identify highly dissimilar regions displaying unusual compositional properties. The application was used to perform a comparative analysis of 50+ microbial genomes as well as many eukaryote genomes including human, rat, mouse, and drosophila. We illustrate the uses of S-Plot in a comparison involving Escherichia coli K12 and E. coli O157:H7.

KW - Escherichia coli K12

KW - Escherichia coli O157:H7

KW - Horizontal gene transfer

KW - Sequence composition

UR - http://www.scopus.com/inward/record.url?scp=33846505986&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33846505986&partnerID=8YFLogxK

U2 - 10.1063/1.2356423

DO - 10.1063/1.2356423

M3 - Conference contribution

AN - SCOPUS:33846505986

VL - 854

SP - 126

EP - 128

BT - AIP Conference Proceedings

ER -