ArticleGenome research1999
Detecting and analyzing DNA sequencing errors: toward a higher quality of the Bacillus subtilis genome sequence.
Article in Genome research, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
19 citing papers in PubMed, 45 citations in OpenAlex.
- Functional interaction between ribosomal protein L6 and RbgA during ribosome assembly.PLoS genetics · 2014Article
- GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences.Nucleic acids research · 2013Article
- Article
- An approach for searching insertions in bacterial genes leading to the phase shift of triplet periodicity.Genomics, proteomics & bioinformatics · 2011Article
- From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later.Microbiology (Reading, England) · 2009Article
- The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.PLoS genetics · 2009Article
- Article
- Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.Genome research · 2008Article
- Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: focus on point miscalls and artefactual expansions.BMC genomics · 2008Article
- Detecting the molecular scars of evolution in the Mycobacterium tuberculosis complex by analyzing interrupted coding sequences.BMC evolutionary biology · 2008Article
- Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition.Genome biology · 2007Article
- Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?Genome biology · 2007Article
- ICDS database: interrupted CoDing sequences in prokaryotic genomes.Nucleic acids research · 2006Article
- MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.Nucleic acids research · 2005Article
- AMIGene: Annotation of MIcrobial Genes.Nucleic acids research · 2003Article
- SubtiList: the reference database for the Bacillus subtilis genome.Nucleic acids research · 2002Article
- From gene regulation to gene function: regulatory networks in bacillus subtilis.Comparative and functional genomics · 2002Article
- Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes.BMC bioinformatics · 2002Article
- Current awareness.Yeast (Chichester, England) · 2000Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
During the determination of a DNA sequence, the introduction of artifactual frameshifts and/or in-frame stop codons in putative genes can lead to misprediction of gene products. Detection of such errors with a method based on protein similarity matching is only possible when related sequences are available in databases. Here, we present a method to detect frameshift errors in DNA sequences that is based on the intrinsic properties of the coding sequences. It combines the results of two analyses, the search for translational initiation/termination sites and the prediction of coding regions. This method was used to screen the complete Bacillus subtilis genome sequence and the regions flanking putative errors were resequenced for verification. This procedure allowed us to correct the sequence and to analyze in detail the nature of the errors. Interestingly, in several cases in-frame termination codons or frameshifts were not sequencing errors but confirmed to be present in the chromosome, indicating that the genes are either nonfunctional (pseudogenes) or subject to regulatory processes such as programmed translational frameshifts. The method can be used for checking the quality of the sequences produced by any prokaryotic genome sequencing project.
Indexed as
Identifiers
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.