EcoGene: A genome sequence database for Escherichia coli K-12

Kenneth E. Rudd

Research output: Contribution to journalArticle

196 Citations (Scopus)

Abstract

The EcoGene database provides a set of gene and protein sequences derived from the genome sequence of Escherichia coli K-12. EcoGene is a source of re-annotated sequences for the SWISS-PROT and Colibri databases. EcoGene is used for genetic and physical map compilations in collaboration with the Coli Genetic Stock Center. The EcoGene12 release includes 4293 genes. EcoGene12 differs from the GenBank annotation of the complete genome sequence in several ways, including (i) the revision of 706 predicted or confirmed gene start sites, (ii) the correction or hypothetical reconstruction of 61 frame-shifts caused by either sequence error or mutation, (iii) the reconstruction of 14 protein sequences interrupted by the insertion of IS elements, and (iv) predictions that 92 genes are partially deleted gene fragments. A literature survey identified 717 proteins whose N-terminal amino acids have been verified by sequencing. 12,446 cross-references to 6835 literature citations and abstracts are provided. EcoGene is accessible at a new website: http://bmb.med.miami.edu/EcoGene/EcoWeb. Users can search and retrieve individual EcoGene GenePages or they can download large datasets for incorporation into database management systems, facilitating various genome-scale computational and functional analyses.

Original languageEnglish
Pages (from-to)60-64
Number of pages5
JournalNucleic Acids Research
Volume28
Issue number1
StatePublished - Jan 1 2000
Externally publishedYes

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Genome
Databases
Escherichia coli
Genes
Database Management Systems
Protein Databases
Proteins
DNA Transposable Elements
Insertional Mutagenesis
Nucleic Acid Databases
Amino Acids
Mutation
Surveys and Questionnaires
Datasets

ASJC Scopus subject areas

  • Genetics

Cite this

EcoGene : A genome sequence database for Escherichia coli K-12. / Rudd, Kenneth E.

In: Nucleic Acids Research, Vol. 28, No. 1, 01.01.2000, p. 60-64.

Research output: Contribution to journalArticle

Rudd, Kenneth E. / EcoGene : A genome sequence database for Escherichia coli K-12. In: Nucleic Acids Research. 2000 ; Vol. 28, No. 1. pp. 60-64.
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