ArticleMicrobial genomics2021
Flanker: a tool for comparative genomics of gene flanking regions.
Article in Microbial genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed, 19 citations in OpenAlex.
- Sarand: exploring antimicrobial resistance gene neighbourhoods in complex metagenomic assembly graphs.NAR genomics and bioinformatics · 2026Article
- Global distribution and genomic characteristics of linezolid resistance gene-positiveFrontiers in microbiology · 2026Article
- Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations.Antimicrobial agents and chemotherapy · 2025Review
- The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study.Nature communications · 2025Article
- External factors influence intrinsic differences in Stx2e production by Porcine Shiga Toxin-producing Escherichia coli strains.PLoS pathogens · 2025Article
- Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria.Nature communications · 2025Article
- The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study.medRxiv : the preprint server for health sciences · 2025Article
- Global genomic epidemiology ofMicrobial genomics · 2024Article
- Genomic investigation of multispecies and multivariantInfection control and hospital epidemiology · 2024Article
- The Genetic Landscape of Antimicrobial Resistance Genes inAntibiotics (Basel, Switzerland) · 2024Article
- The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies.Nature communications · 2024Article
- Phenotypic and genotypic assessment of iron acquisition in diverse bovine-associated non-aureus staphylococcal strains.Veterinary research · 2024Article
- Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis.Microbiology spectrum · 2024Article
- Visualizing and quantifying structural diversity around mobile resistance genes.Microbial genomics · 2023Article
- Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer.Nature communications · 2023Article
- Article
- Detection of maternal transmission of resistant Gram-negative bacteria in a Cambodian hospital setting.Frontiers in microbiology · 2023Article
- Global Distribution ofmSystems · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
Analysing the flanking sequences surrounding genes of interest is often highly relevant to understanding the role of mobile genetic elements (MGEs) in horizontal gene transfer, particular for antimicrobial-resistance genes. Here, we present Flanker, a Python package that performs alignment-free clustering of gene flanking sequences in a consistent format, allowing investigation of MGEs without prior knowledge of their structure. These clusters, known as 'flank patterns' (FPs), are based on Mash distances, allowing for easy comparison of similarity across sequences. Additionally, Flanker can be flexibly parameterized to fine-tune outputs by characterizing upstream and downstream regions separately, and investigating variable lengths of flanking sequence. We apply Flanker to two recent datasets describing plasmid-associated carriage of important carbapenemase genes (
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.