ArticleBMC bioinformatics2008
Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 54 citations in OpenAlex.
- Molecular kinetics dictate population dynamics in CRISPR-based plasmid defense.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals.Nature communications · 2025Article
- SHIP: identifying antimicrobial resistance gene transfer between plasmids.Bioinformatics (Oxford, England) · 2023Article
- Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission.The ISME journal · 2023Article
- Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils.The ISME journal · 2021Article
- GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level.BMC genomics · 2021Article
- Article
- Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins.Microbial genomics · 2018Article
- Bipartite Network Analysis of Gene Sharings in the Microbial World.Molecular biology and evolution · 2018Article
- Identification of Plasmid-Encoded sRNAs in aFrontiers in microbiology · 2018Article
- Article
- Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology.Frontiers in microbiology · 2017Article
- Analysis of a Pool of Small Plasmids from Soil Heterotrophic Cultivable Bacterial Communities.The open microbiology journal · 2015Article
- Modularized evolution in archaeal methanogens phylogenetic forest.Genome biology and evolution · 2014Article
- Network Analysis of Plasmidomes: The Azospirillum brasilense Sp245 Case.International journal of evolutionary biology · 2014Article
- Salmonella pathogenicity and host adaptation in chicken-associated serovars.Microbiology and molecular biology reviews : MMBR · 2013Review
- Using protein clusters from whole proteomes to construct and augment a dendrogram.Advances in bioinformatics · 2013Article
- Goods-thinking vs. tree-thinking: Finding a place for mobile genetic elements.Mobile genetic elements · 2011Article
- The mosaicism of plasmids revealed by atypical genes detection and analysis.BMC genomics · 2011Article
- Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.Biology direct · 2011Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPhylogenetic methods are well-established bioinformatic tools for sequence analysis, allowing to describe the non-independencies of sequences because of their common ancestor. However, the evolutionary profiles of bacterial genes are often complicated by hidden paralogy and extensive and/or (multiple) horizontal gene transfer (HGT) events which make bifurcating trees often inappropriate. In this context, plasmid sequences are paradigms of network-like relationships characterizing the evolution of prokaryotes. Actually, they can be transferred among different organisms allowing the dissemination of novel functions, thus playing a pivotal role in prokaryotic evolution. However, the study of their evolutionary dynamics is complicated by the absence of universally shared genes, a prerequisite for phylogenetic analyses.
resultsTo overcome such limitations we developed a bioinformatic package, named Blast2Network (B2N), allowing the automatic phylogenetic profiling and the visualization of homology relationships in a large number of plasmid sequences. The software was applied to the study of 47 completely sequenced plasmids coming from Escherichia, Salmonella and Shigella spps.
conclusionThe tools implemented by B2N allow to describe and visualize in a new way some of the evolutionary features of plasmid molecules of Enterobacteriaceae; in particular it helped to shed some light on the complex history of Escherichia, Salmonella and Shigella plasmids and to focus on possible roles of unannotated proteins.The proposed methodology is general enough to be used for comparative genomic analyses of bacteria.
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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.