ArticleArchives of microbiology2008
Genome information management and integrated data analysis with HaloLex.
Article in Archives of microbiology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
54 citing papers in PubMed.
- Characterization of aliA and aliB deletion mutants reveals a dominant role of AliA in Haloferax volcanii lipoprotein lipidation.The Journal of biological chemistry · 2026Article
- Proteome characterization of single gene deletion mutants lacking zinc finger µ-proteins inmicroLife · 2026Article
- Archaea express circular isoforms of IS200/IS605-associated ωRNAs.Frontiers in microbiology · 2025Article
- Studying the long-term adaptation ofFrontiers in microbiology · 2025Article
- Elucidating metabolic pathways through genomic analysis in highly heavy metal-resistantHeliyon · 2024Article
- Intermolecular Gene Conversion for the Equalization of Genome Copies in the Polyploid HaloarchaeonGenes · 2024Article
- C(P)XCG Proteins ofInternational journal of molecular sciences · 2024Article
- Iron starvation results in up-regulation of a probableFrontiers in microbiology · 2024Article
- Characterization of the zinc finger μ-protein HVO_0758 fromFrontiers in microbiology · 2023Article
- Comparative Analysis of rRNA Removal Methods for RNA-Seq Differential Expression in Halophilic Archaea.Biomolecules · 2022Article
- The archaeal classFrontiers in microbiology · 2022Article
- Proteome Turnover Analysis in Haloferax volcanii by a Heavy Isotope Multilabeling Approach.Methods in molecular biology (Clifton, N.J.) · 2022Article
- CdrS Is a Global Transcriptional Regulator Influencing Cell Division in Haloferax volcanii.mBio · 2021Article
- Open Issues for Protein Function Assignment inGenes · 2021Article
- Elucidation of the Translation Initiation Factor Interaction Network ofFrontiers in microbiology · 2021Article
- Characterization of Non-selected Intermolecular Gene Conversion in the Polyploid HaloarchaeonFrontiers in microbiology · 2021Article
- Regulated Iron Siderophore Production of the Halophilic ArchaeonBiomolecules · 2020Article
- The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics.Nature communications · 2020Article
- Identification of RNA 3´ ends and termination sites inRNA biology · 2020Article
- Whole-genome comparison between the type strain of Halobacterium salinarum (DSM 3754MicrobiologyOpen · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HaloLex is a software system for the central management, integration, curation, and web-based visualization of genomic and other -omics data for any given microorganism. The system has been employed for the manual curation of three haloarchaeal genomes, namely Halobacterium salinarum (strain R1), Natronomonas pharaonis, and Haloquadratum walsbyi. HaloLex, in particular, enables the integrated analysis of genome-wide proteomic results with the underlying genomic data. This has proven indispensable to generate reliable gene predictions for GC-rich genomes, which, due to their characteristically low abundance of stop codons, are known to be hard targets for standard gene finders, especially concerning start codon assignment. The proteomic identification of more than 600 N-terminal peptides has greatly increased the reliability of the start codon assignment for Halobacterium salinarum. Application of homology-based methods to the published genome of Haloarcula marismortui allowed to detect 47 previously unidentified genes (a problem that is particularly serious for short protein sequences) and to correct more than 300 start codon misassignments.
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What OpenQuestion holds
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.