ArticleBMC genomics2007
Optical mapping as a routine tool for bacterial genome sequence finishing.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 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
68 citing papers in PubMed, 99 citations in OpenAlex.
- The genome of a steinernematid-associatedAccess microbiology · 2023Article
- Genomic Degeneration and Reduction in the Fish PathogenMicrobiology spectrum · 2022Article
- Progress in Methods for Copy Number Variation Profiling.International journal of molecular sciences · 2022Review
- Customized optical mapping by CRISPR-Cas9 mediated DNA labeling with multiple sgRNAs.Nucleic acids research · 2021Article
- Advances in optical mapping for genomic research.Computational and structural biotechnology journal · 2020Review
- Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes.Scientific reports · 2019Article
- A micropatterned substrate for on-surface enzymatic labelling of linearized long DNA molecules.Scientific reports · 2019Article
- Whole-genome sequence data and analysis ofData in brief · 2019Article
- Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition byFrontiers in microbiology · 2018Article
- The first draft reference genome of the American mink (Neovison vison).Scientific reports · 2017Article
- Article
- Complete Genome Sequence of the Sourdough IsolateGenome announcements · 2017Article
- Complete Genome Sequence ofGenome announcements · 2017Article
- Whole-Genome Sequence of the Cheese Isolate Lactobacillus rennini ACA-DC 565.Genome announcements · 2017Article
- Complete Genome Sequence of the Dairy Isolate Lactobacillus acidipiscis ACA-DC 1533.Genome announcements · 2017Article
- Article
- Transcriptomics-driven lipidomics (TDL) identifies the microbiome-regulated targets of ileal lipid metabolism.NPJ systems biology and applications · 2017Article
- SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.BMC bioinformatics · 2016Article
- Complete Genome Sequence of Lactococcus lactis subsp. lactis A12, a Strain Isolated from Wheat Sourdough.Genome announcements · 2016Article
- Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002.BMC genomics · 2016Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 10 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 99.9% identical between the plasmid and chromosome of X. nematophila.
resultsWhole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished.
conclusionOur experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly.
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.