ArticleNucleic acids research1994
Intrinsic and extrinsic approaches for detecting genes in a bacterial genome.
Article in Nucleic acids research, 1994. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 101 citations in OpenAlex.
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- BASys2: a next-generation bacterial genome annotation system.Nucleic acids research · 2025Article
- Comparative Analysis and Structural Modeling ofBiology · 2022Article
- Prokaryotic Genome Annotation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Evolution of Microbial Genomics: Conceptual Shifts over a Quarter Century.Trends in microbiology · 2021Review
- EcoGene 3.0.Nucleic acids research · 2013Article
- Article
- Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.Viruses · 2010Article
- VIGOR, an annotation program for small viral genomes.BMC bioinformatics · 2010Article
- Molecular interactions of Escherichia coli ExoIX and identification of its associated 3'-5' exonuclease activity.Nucleic acids research · 2007Article
- Improving gene annotation of complete viral genomes.Nucleic acids research · 2003Article
- Current methods of gene prediction, their strengths and weaknesses.Nucleic acids research · 2002Review
- The Yersinia enterocolitica phospholipase gene yplA is part of the flagellar regulon.Journal of bacteriology · 2000Article
- Active-site mutations in the Xrn1p exoribonuclease of Saccharomyces cerevisiae reveal a specific role in meiosis.Molecular and cellular biology · 1999Article
- Identification and characterization of a new lipoprotein, NlpI, in Escherichia coli K-12.Journal of bacteriology · 1999Article
- Role in cell permeability of an essential two-component system in Staphylococcus aureus.Journal of bacteriology · 1999Article
- Acid- and base-induced proteins during aerobic and anaerobic growth of Escherichia coli revealed by two-dimensional gel electrophoresis.Journal of bacteriology · 1999Article
- Computational methods for exon detection.Molecular biotechnology · 1998Review
- Combining diverse evidence for gene recognition in completely sequenced bacterial genomes.Nucleic acids research · 1998Article
- Compilation of DNA sequences of Escherichia coli K12: description of the interactive databases ECD and ECDC.Nucleic acids research · 1998Article
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3 authors at 1 institution in 1 country.
Funding
Abstract
The unannotated regions of the Escherichia coli genome DNA sequence from the EcoSeq6 database, totaling 1,278 'intergenic' sequences of the combined length of 359,279 basepairs, were analyzed using computer-assisted methods with the aim of identifying putative unknown genes. The proposed strategy for finding new genes includes two key elements: i) prediction of expressed open reading frames (ORFs) using the GeneMark method based on Markov chain models for coding and non-coding regions of Escherichia coli DNA, and ii) search for protein sequence similarities using programs based on the BLAST algorithm and programs for motif identification. A total of 354 putative expressed ORFs were predicted by GeneMark. Using the BLASTX and TBLASTN programs, it was shown that 208 ORFs located in the unannotated regions of the E. coli chromosome are significantly similar to other protein sequences. Identification of 182 ORFs as probable genes was supported by GeneMark and BLAST, comprising 51.4% of the GeneMark 'hits' and 87.5% of the BLAST 'hits'. 73 putative new genes, comprising 20.6% of the GeneMark predictions, belong to ancient conserved protein families that include both eubacterial and eukaryotic members. This value is close to the overall proportion of highly conserved sequences among eubacterial proteins, indicating that the majority of the putative expressed ORFs that are predicted by GeneMark, but have no significant BLAST hits, nevertheless are likely to be real genes. The majority of the putative genes identified by BLAST search have been described since the release of the EcoSeq6 database, but about 70 genes have not been detected so far. Among these new identifications are genes encoding proteins with a variety of predicted functions including dehydrogenases, kinases, several other metabolic enzymes, ATPases, rRNA methyltransferases, membrane proteins, and different types of regulatory proteins.
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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.