Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map

Kenneth E. Rudd, Webb Miller, James Ostell, Dennis A. Benson

Research output: Contribution to journalArticle

60 Citations (Scopus)

Abstract

We use the extensive published information describing the genome of Escherichia coli and new restriction map alignment software to align DNA sequence, genetic, and physical maps. Restriction map alignment software is used which considers restriction maps as strings analogous to DNA or protein sequences except that two values, enzyme name and DNA base address, are associated with each position on the string. The resulting alignments reveal a nearly linear relationship between the physical and genetic maps of the E. coli chromosome. Physical map comparisons with the 1976, 1980, and 1983 genetic maps demonstrate a better fit with the more recent maps. The results of these alignments are genomic kilobase coordinates, orientation and rank of the alignment that best fits the genetic data. A statistical measure based on extreme value distribution is applied to the alignments. Additional computer analyses allow us to estimate the accuracy of the published E. coli genomic restriction map, simulate rearrangements of the bacterial chromosome, and search for repetitive DNA. The procedures we used are general enough to be applicable to other genome mapping projects.

Original languageEnglish
Pages (from-to)313-321
Number of pages9
JournalNucleic Acids Research
Volume18
Issue number2
StatePublished - Jan 25 1990
Externally publishedYes

Fingerprint

Escherichia coli K12
DNA sequences
DNA Sequence
Escherichia coli
Escherichia Coli
Genomics
Alignment
Restriction
DNA
Software
Bacterial Chromosomes
Chromosome Mapping
Names
Chromosomes
Genome
Chromosome
Enzymes
Genes
Strings
Proteins

ASJC Scopus subject areas

  • Genetics
  • Statistics, Probability and Uncertainty
  • Applied Mathematics
  • Health, Toxicology and Mutagenesis
  • Toxicology
  • Genetics(clinical)

Cite this

Rudd, K. E., Miller, W., Ostell, J., & Benson, D. A. (1990). Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map. Nucleic Acids Research, 18(2), 313-321.

Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map. / Rudd, Kenneth E.; Miller, Webb; Ostell, James; Benson, Dennis A.

In: Nucleic Acids Research, Vol. 18, No. 2, 25.01.1990, p. 313-321.

Research output: Contribution to journalArticle

Rudd, KE, Miller, W, Ostell, J & Benson, DA 1990, 'Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map', Nucleic Acids Research, vol. 18, no. 2, pp. 313-321.
Rudd KE, Miller W, Ostell J, Benson DA. Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map. Nucleic Acids Research. 1990 Jan 25;18(2):313-321.
Rudd, Kenneth E. ; Miller, Webb ; Ostell, James ; Benson, Dennis A. / Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map. In: Nucleic Acids Research. 1990 ; Vol. 18, No. 2. pp. 313-321.
@article{2e0316059d9149cdac3565fa6c4f572a,
title = "Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map",
abstract = "We use the extensive published information describing the genome of Escherichia coli and new restriction map alignment software to align DNA sequence, genetic, and physical maps. Restriction map alignment software is used which considers restriction maps as strings analogous to DNA or protein sequences except that two values, enzyme name and DNA base address, are associated with each position on the string. The resulting alignments reveal a nearly linear relationship between the physical and genetic maps of the E. coli chromosome. Physical map comparisons with the 1976, 1980, and 1983 genetic maps demonstrate a better fit with the more recent maps. The results of these alignments are genomic kilobase coordinates, orientation and rank of the alignment that best fits the genetic data. A statistical measure based on extreme value distribution is applied to the alignments. Additional computer analyses allow us to estimate the accuracy of the published E. coli genomic restriction map, simulate rearrangements of the bacterial chromosome, and search for repetitive DNA. The procedures we used are general enough to be applicable to other genome mapping projects.",
author = "Rudd, {Kenneth E.} and Webb Miller and James Ostell and Benson, {Dennis A.}",
year = "1990",
month = "1",
day = "25",
language = "English",
volume = "18",
pages = "313--321",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "2",

}

TY - JOUR

T1 - Alignment of Escherichia coli K12 DNA sequences to a genomic restriction map

AU - Rudd, Kenneth E.

AU - Miller, Webb

AU - Ostell, James

AU - Benson, Dennis A.

PY - 1990/1/25

Y1 - 1990/1/25

N2 - We use the extensive published information describing the genome of Escherichia coli and new restriction map alignment software to align DNA sequence, genetic, and physical maps. Restriction map alignment software is used which considers restriction maps as strings analogous to DNA or protein sequences except that two values, enzyme name and DNA base address, are associated with each position on the string. The resulting alignments reveal a nearly linear relationship between the physical and genetic maps of the E. coli chromosome. Physical map comparisons with the 1976, 1980, and 1983 genetic maps demonstrate a better fit with the more recent maps. The results of these alignments are genomic kilobase coordinates, orientation and rank of the alignment that best fits the genetic data. A statistical measure based on extreme value distribution is applied to the alignments. Additional computer analyses allow us to estimate the accuracy of the published E. coli genomic restriction map, simulate rearrangements of the bacterial chromosome, and search for repetitive DNA. The procedures we used are general enough to be applicable to other genome mapping projects.

AB - We use the extensive published information describing the genome of Escherichia coli and new restriction map alignment software to align DNA sequence, genetic, and physical maps. Restriction map alignment software is used which considers restriction maps as strings analogous to DNA or protein sequences except that two values, enzyme name and DNA base address, are associated with each position on the string. The resulting alignments reveal a nearly linear relationship between the physical and genetic maps of the E. coli chromosome. Physical map comparisons with the 1976, 1980, and 1983 genetic maps demonstrate a better fit with the more recent maps. The results of these alignments are genomic kilobase coordinates, orientation and rank of the alignment that best fits the genetic data. A statistical measure based on extreme value distribution is applied to the alignments. Additional computer analyses allow us to estimate the accuracy of the published E. coli genomic restriction map, simulate rearrangements of the bacterial chromosome, and search for repetitive DNA. The procedures we used are general enough to be applicable to other genome mapping projects.

UR - http://www.scopus.com/inward/record.url?scp=0025124530&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0025124530&partnerID=8YFLogxK

M3 - Article

C2 - 2183179

AN - SCOPUS:0025124530

VL - 18

SP - 313

EP - 321

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 2

ER -