ArticleNucleic acids research2000
EcoGene: a genome sequence database for Escherichia coli K-12.
Article in Nucleic acids research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
116 citing papers in PubMed.
- Genomic language models (gLMs) decode bacterial genomes for improved gene prediction and translation initiation site identification.Briefings in bioinformatics · 2025Article
- Automated characterization and analysis of expression compatibility between regulatory sequences and metabolic genes inSynthetic and systems biotechnology · 2024Article
- Escherichia coli cell factories with altered chromosomal replication scenarios exhibit accelerated growth and rapid biomass production.Microbial cell factories · 2022Article
- Identification of conserved slow codons that are important for protein expression and function.RNA biology · 2021Article
- A Genome-Scale Antibiotic Screen in Serratia marcescens Identifies YdgH as a Conserved Modifier of Cephalosporin and Detergent Susceptibility.Antimicrobial agents and chemotherapy · 2021Article
- Comparative genomic analysis ofMicrobial genomics · 2021Article
- StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes.Frontiers in bioinformatics · 2021Review
- DrpB (YedR) Is a Nonessential Cell Division Protein in Escherichia coli.Journal of bacteriology · 2020Article
- Genome-wide high-throughput screening of interactive bacterial metabolite in the algal population using Escherichia coli K-12 Keio collection.Scientific reports · 2020Article
- The Regulation of Bacterial Biofilm Formation by cAMP-CRP: A Mini-Review.Frontiers in microbiology · 2020Review
- Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.Genome research · 2018Article
- High-yield production of 1,3-propanediol from glycerol by metabolically engineeredBiotechnology for biofuels · 2018Article
- Review
- The Highly ConservedFrontiers in microbiology · 2016Article
- Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb).Molecular & cellular proteomics : MCP · 2014Article
- Evolution of a genome-encoded bias in amino acid biosynthetic pathways is a potential indicator of amino acid dynamics in the environment.Molecular biology and evolution · 2014Article
- Curli biogenesis: order out of disorder.Biochimica et biophysica acta · 2014Review
- Stochastic EM-based TFBS motif discovery with MITSU.Bioinformatics (Oxford, England) · 2014Article
- Thermodynamic modeling of variations in the rate of RNA chain elongation of E. coli rrn operons.Biophysical journal · 2014Article
- DEOP: a database on osmoprotectants and associated pathways.Database : the journal of biological databases and curation · 2014Article
56 more citing papers are in PubMed but not listed here.
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
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) pre-dictions 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 s 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.