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Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare

https://doi.org/10.1101/2020.10.16.342287

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/0962-8479(95)90533-2openalex-snapshot

IS6110 restriction fragment length polymorphism typing of clinical isolates of Mycobacterium tuberculosis from patients with pulmonary tuberculosis in Madras, South India

inferredcites →https://doi.org/10.1016/j.resmic.2003.12.008openalex-snapshot

Dynamics of insertion sequence elements during experimental evolution of bacteria

inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot

Basic Local Alignment Search Tool

inferredcites →https://doi.org/10.1021/acssynbio.9b00218openalex-snapshot

Defensive Function of Transposable Elements in Bacteria

inferredcites →https://doi.org/10.1038/nrmicro3235openalex-snapshot

Bordetella pertussis pathogenesis: current and future challenges

inferredcites →https://doi.org/10.1080/1040841x.2017.1303661openalex-snapshot

The impact of insertion sequences on bacterial genome plasticity and adaptability

inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

inferredcites →https://doi.org/10.1093/bib/bbw096openalex-snapshot

The present and future ofde novowhole-genome assembly

inferredcites →https://doi.org/10.1093/bioinformatics/btaa213openalex-snapshot

DNA Features Viewer: a sequence annotation formatting and plotting library for Python

inferredcites →https://doi.org/10.1093/bioinformatics/btp163openalex-snapshot

Biopython: freely available Python tools for computational molecular biology and bioinformatics

inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot

Prokka: rapid prokaryotic genome annotation

inferredcites →https://doi.org/10.1093/bioinformatics/btv388openalex-snapshot

ISQuest: finding insertion sequences in prokaryotic sequence fragment data

inferredcites →https://doi.org/10.1093/bioinformatics/btx433openalex-snapshot

ISEScan: automated identification of insertion sequence elements in prokaryotic genomes

inferredcites →https://doi.org/10.1093/bioinformatics/bty479openalex-snapshot

panISa: ab initio detection of insertion sequences in bacterial genomes from short read sequence data

inferredcites →https://doi.org/10.1093/dnares/dst014openalex-snapshot

Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011

inferredcites →https://doi.org/10.1093/femspd/ftv064openalex-snapshot

Bordetella pertussisevolution in the (functional) genomics era

inferredcites →https://doi.org/10.1093/nar/gkj014openalex-snapshot

ISfinder: the reference centre for bacterial insertion sequences

inferredcites →https://doi.org/10.1093/nar/gks778openalex-snapshot

OASIS: an automated program for global investigation of bacterial and archaeal insertion sequences

inferredcites →https://doi.org/10.1093/nar/gkv1118openalex-snapshot

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

inferredcites →https://doi.org/10.1093/nar/gkv1226openalex-snapshot

Assembly: a resource for assembled genomes at NCBI

inferredcites →https://doi.org/10.1093/nar/gkw343openalex-snapshot

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

inferredcites →https://doi.org/10.1093/nar/gkz239openalex-snapshot

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

inferredcites →https://doi.org/10.1093/pcp/pcq114openalex-snapshot

The bacA Gene Homolog, mlr7400, in Mesorhizobium loti MAFF303099 is Dispensable for Symbiosis with Lotus japonicus but Partially Capable of Supporting the Symbiotic Function of bacA in Sinorhizobium meliloti

inferredcites →https://doi.org/10.1099/ijs.0.64483-0openalex-snapshot

DNA–DNA hybridization values and their relationship to whole-genome sequence similarities

inferredcites →https://doi.org/10.1099/mgen.0.000062openalex-snapshot

Quantitative assessment of insertion sequence impact on bacterial genome architecture

inferredcites →https://doi.org/10.1099/mgen.0.000180openalex-snapshot

Bordetella pertussis population dynamics and phylogeny in Japan after adoption of acellular pertussis vaccines

inferredcites →https://doi.org/10.1109/mcse.2010.145openalex-snapshot

Automatic Lip-Contour Extraction and Mouth-Structure Segmentation in Images

inferredcites →https://doi.org/10.1109/mcse.2011.37openalex-snapshot

The NumPy Array: A Structure for Efficient Numerical Computation

inferredcites →https://doi.org/10.1111/1574-6976.12067openalex-snapshot

Bacterial insertion sequences: their genomic impact and diversity

inferredcites →https://doi.org/10.1128/aem.01001-10openalex-snapshot

Evolutionary Dynamics of Insertion Sequences in Relation to the Evolutionary Histories of the Chromosome and Symbiotic Plasmid Genes of Rhizobium etli Populations

inferredcites →https://doi.org/10.1128/cvi.00717-13openalex-snapshot

Prevalence and Molecular Characterization of Pertactin-Deficient Bordetella pertussis in the United States

inferredcites →https://doi.org/10.1128/iai.00188-10openalex-snapshot

Pertactin Is Required forBordetellaSpecies To Resist Neutrophil-Mediated Clearance

inferredcites →https://doi.org/10.1128/jb.01258-08openalex-snapshot

Functional Analysis of Insertion Sequence IS Aba1 , Responsible for Genomic Plasticity of Acinetobacter baumannii

inferredcites →https://doi.org/10.1128/jcm.34.6.1453-1461.1996openalex-snapshot

DNA fingerprinting of Vibrio cholerae strains with a novel insertion sequence element: a tool to identify epidemic strains

inferredcites →https://doi.org/10.1128/jcm.42.12.5462-5466.2004openalex-snapshot

Development of a Rapid PCR Method Using the Insertion Sequence IS 1203 for Genotyping Shiga Toxin-Producing Escherichia coli O157

inferredcites →https://doi.org/10.1128/mbio.00505-19openalex-snapshot

Codon Usage Heterogeneity in the Multipartite Prokaryote Genome: Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry

inferredcites →https://doi.org/10.1128/mbio.01074-14openalex-snapshot

Global Population Structure and Evolution of Bordetella pertussis and Their Relationship with Vaccination

inferredcites →https://doi.org/10.1128/mbio.02579-19openalex-snapshot

Drug-Resistant Epimutants Exhibit Organ-Specific Stability and Induction during Murine Infections Caused by the Human Fungal Pathogen Mucor circinelloides

inferredcites →https://doi.org/10.1128/mmbr.62.3.725-774.1998openalex-snapshot

Insertion Sequences

inferredcites →https://doi.org/10.1186/1471-2105-15-71openalex-snapshot

Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements

inferredcites →https://doi.org/10.1186/1471-2164-15-1039openalex-snapshot

Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq

inferredcites →https://doi.org/10.1186/1471-2164-16-1openalex-snapshot

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

inferredcites →https://doi.org/10.1186/s12864-015-1860-2openalex-snapshot

ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data

inferredcites →https://doi.org/10.1186/s12864-015-2294-6openalex-snapshot

Locating rearrangement events in a phylogeny based on highly fragmented assemblies

inferredcites →https://doi.org/10.1186/s12864-016-2878-9openalex-snapshot

The early events underlying genome evolution in a localized Sinorhizobium meliloti population

inferredcites →https://doi.org/10.3201/eid2304.161575openalex-snapshot

Significant Decrease in Pertactin-Deficient Bordetella pertussis Isolates, Japan

inferredcites →https://doi.org/10.3201/eid2511.190329openalex-snapshot

Rare Detection ofBordetella pertussisPertactin-Deficient Strains in Argentina

inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot

R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.3389/fmicb.2018.00627openalex-snapshot

Contribution of Mobile Group II Introns to Sinorhizobium meliloti Genome Evolution

inferredcites →https://doi.org/10.3389/fmicb.2018.00803openalex-snapshot

Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution

inferredcites →https://doi.org/10.3390/vaccines8020217openalex-snapshot

Acellular Pertussis Vaccine Components: Today and Tomorrow

inferredcites →https://doi.org/10.4056/sigs.541628openalex-snapshot

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1128/mbio.02060-21openalex-snapshot

TnCentral: a Prokaryotic Transposable Element Database and Web Portal for Transposon Analysis

inferred← citeshttps://doi.org/10.70675/8d78267cz6084z4476z97cdz117b0db8f081openalex-snapshot

Diversité phénotypique et moléculaire d'isolats urinaires de Pseudomonas aeruginosa

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