Mapping sequenced E.coli genes by computer

Software, strategies and examples

Kenneth E. Rudd, Webb Miller, Craig Werner, James Ostell, Carolyn Tolstoshev, Steven G. Satterfield

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

Methods are presented for organizing and integrating DNA sequence data, restriction maps, and genetic maps for the same organism but from a variety of sources (databases, publications, personal communications). Proper software tools are essential for successful organization of such diverse data into an ordered, cohesive body of information, and a suite of novel software to support this endeavor is described. Though these tools automate much of the task, a variety of strategies is needed to cope with recalcitrant cases. We describe such strategies and illustrate their application with numerous examples. These strategies have allowed us to order, analyze, and display over one megabase of E. coli DNA sequence information. The integration task often exposes inconsistencies in the available data, perhaps caused by strain polymorphisms or human oversight, necessitating the application of sound biological judgment. The examples illustrate both the level of expertise required of the database curator and the knowledge gained as apparent inconsistencies are resolved. The software and mapping methods are applicable to the study of any genome for which a high resolution restriction map is available. They were developed to support a weakly coordinated sequencing effort involving many laboratories, but would also be useful for highly orchestrated sequencing projects.

Original languageEnglish
Pages (from-to)637-647
Number of pages11
JournalNucleic Acids Research
Volume19
Issue number3
StatePublished - Feb 11 1991
Externally publishedYes

Fingerprint

Escherichia coli
Escherichia Coli
Software
Genes
DNA sequences
Gene
Inconsistency
DNA Sequence
Databases
Sequencing
Cellular telephone systems
Restriction
Polymorphism
Publications
Expertise
Software Tools
Display devices
Communication
Acoustic waves
Genome

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., Werner, C., Ostell, J., Tolstoshev, C., & Satterfield, S. G. (1991). Mapping sequenced E.coli genes by computer: Software, strategies and examples. Nucleic Acids Research, 19(3), 637-647.

Mapping sequenced E.coli genes by computer : Software, strategies and examples. / Rudd, Kenneth E.; Miller, Webb; Werner, Craig; Ostell, James; Tolstoshev, Carolyn; Satterfield, Steven G.

In: Nucleic Acids Research, Vol. 19, No. 3, 11.02.1991, p. 637-647.

Research output: Contribution to journalArticle

Rudd, KE, Miller, W, Werner, C, Ostell, J, Tolstoshev, C & Satterfield, SG 1991, 'Mapping sequenced E.coli genes by computer: Software, strategies and examples', Nucleic Acids Research, vol. 19, no. 3, pp. 637-647.
Rudd KE, Miller W, Werner C, Ostell J, Tolstoshev C, Satterfield SG. Mapping sequenced E.coli genes by computer: Software, strategies and examples. Nucleic Acids Research. 1991 Feb 11;19(3):637-647.
Rudd, Kenneth E. ; Miller, Webb ; Werner, Craig ; Ostell, James ; Tolstoshev, Carolyn ; Satterfield, Steven G. / Mapping sequenced E.coli genes by computer : Software, strategies and examples. In: Nucleic Acids Research. 1991 ; Vol. 19, No. 3. pp. 637-647.
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