ArticleNucleic acids research2003
A revised annotation and comparative analysis of Helicobacter pylori genomes.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 86 citations in OpenAlex.
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- Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets.The Journal of biological chemistry · 2017Article
- Role of the N-Acetylmuramoyl-l-Alanyl Amidase, AmiA, of Helicobacter pylori in Peptidoglycan Metabolism, Daughter Cell Separation, and Virulence.Microbial drug resistance (Larchmont, N.Y.) · 2016Article
- Staphylococcus aureus Survives with a Minimal Peptidoglycan Synthesis Machine but Sacrifices Virulence and Antibiotic Resistance.PLoS pathogens · 2015Article
- Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution.Nucleic acids research · 2015Article
- Helicobacter pylori: bacterial strategy for incipient stage and persistent colonization in human gastric niches.Yonsei medical journal · 2014Article
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- DprB facilitates inter- and intragenomic recombination in Helicobacter pylori.Journal of bacteriology · 2012Article
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- CAMBer: an approach to support comparative analysis of multiple bacterial strains.BMC genomics · 2011Article
- Complexomics study of two Helicobacter pylori strains of two pathological origins: potential targets for vaccine development and new insight in bacteria metabolism.Molecular & cellular proteomics : MCP · 2010Article
- Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer.Nucleic acids research · 2010Article
- The HP0256 gene product is involved in motility and cell envelope architecture of Helicobacter pylori.BMC microbiology · 2010Article
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- Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen.BMC genomics · 2010Article
- In Helicobacter pylori, LuxS is a key enzyme in cysteine provision through a reverse transsulfuration pathway.Journal of bacteriology · 2010Article
- A protocol for generating a high-quality genome-scale metabolic reconstruction.Nature protocols · 2010Article
- A variable gene in a conserved region of the Helicobacter pylori genome: isotopic gene replacement or rapid evolution?DNA research : an international journal for rapid publication of reports on genes and genomes · 2008Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Huge amounts of genomic information are currently being generated. Therefore, biologists require structured, exhaustive and comparative databases. The PyloriGene database (http://genolist.pasteur.fr/PyloriGene) was developed to respond to these needs, by integrating and connecting the information generated during the sequencing of two distinct strains of Helicobacter pylori. This led to the need for a general annotation consensus, as the physical and functional annotations of the two strains differed significantly in some cases. A revised functional classification system was created to accommodate the existing data and to make it possible to classify coding sequences (CDS) into several functional categories to harmonize CDS classification. The annotation of the two complete genomes was revised in the light of new data, allowing us to reduce the percentage of hypothetical proteins from approximately 40 to 33%. This resulted in the reassignment of functions for 108 CDS (approximately 7% of all CDS). Interestingly, the functions of only approximately 13% of CDS (222 out of 1658 CDS) were annotated as a result of work done directly on H.pylori genes. Finally, comparison of the two published genomes revealed a significant amount of size variation between corresponding (orthologous) CDS. Most of these size variations were due to natural polymorphisms, although other sources of variation were identified, such as pseudogenes, new genes potentially regulated by slipped-strand mispairing mechanism, or frame-shifts. 113 of these differences were due to different start codon assignments, a common problem when constructing physical annotations.
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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.