ArticleBriefings in bioinformatics2017
Zisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties.
Article in Briefings in bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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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.
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Who cites it
28 citing papers in PubMed, 49 citations in OpenAlex.
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- Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins.Database : the journal of biological databases and curation · 2022Article
- Comparative Genome Analysis Reveals Phylogenetic Identity of Bacillus velezensis HNA3 and Genomic Insights into Its Plant Growth Promotion and Biocontrol Effects.Microbiology spectrum · 2022Article
- A Type VI Secretion System Facilitates Fitness, Homeostasis, and Competitive Advantages for Environmental Adaptability and Efficient Nicotine Biodegradation.Applied and environmental microbiology · 2021Article
- Prediction and AnalysisFrontiers in microbiology · 2021Article
- Genomic Island Prediction via Chi-Square Test and Random Forest Algorithm.Computational and mathematical methods in medicine · 2021Article
- Experimental approaches to tracking mobile genetic elements in microbial communities.FEMS microbiology reviews · 2020Review
- New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements.Nucleic acids research · 2020Article
- IslandCafe: Compositional Anomaly and Feature Enrichment Assessment for Delineation of Genomic Islands.G3 (Bethesda, Md.) · 2019Article
- Microbial genomic island discovery, visualization and analysis.Briefings in bioinformatics · 2019Review
- Virulence factor landscape of a Staphylococcus aureus sequence type 45 strain, MCRF184.BMC genomics · 2019Article
- Whole-genome sequencing and comparative analysis of two plant-associated strains of Rhodopseudomonas palustris (PS3 and YSC3).Scientific reports · 2018Article
- Mutation Landscape of Base Substitutions, Duplications, and Deletions in the Representative Current Cholera Pandemic Strain.Genome biology and evolution · 2018Article
- Improved genomic island predictions with IslandPath-DIMOB.Bioinformatics (Oxford, England) · 2018Article
- MTGIpick allows robust identification of genomic islands from a single genome.Briefings in bioinformatics · 2018Article
- xenoGI: reconstructing the history of genomic island insertions in clades of closely related bacteria.BMC bioinformatics · 2018Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
Genomic islands are genomic fragments of alien origin in bacterial and archaeal genomes, usually involved in symbiosis or pathogenesis. In this work, we described Zisland Explorer, a novel tool to predict genomic islands based on the segmental cumulative GC profile. Zisland Explorer was designed with a novel strategy, as well as a combination of the homogeneity and heterogeneity of genomic sequences. While the sequence homogeneity reflects the composition consistence within each island, the heterogeneity measures the composition bias between an island and the core genome. The performance of Zisland Explorer was evaluated on the data sets of 11 different organisms. Our results suggested that the true-positive rate (TPR) of Zisland Explorer was at least 10.3% higher than that of four other widely used tools. On the other hand, the new tool did not lose overall accuracy with the improvement in the TPR and showed better equilibrium among various evaluation indexes. Also, Zisland Explorer showed better accuracy in the prediction of experimental island data. Overall, the tool provides an alternative solution over other tools, which expands the field of island prediction and offers a supplement to increase the performance of the distinct predicting strategy. We have provided a web service as well as a graphical user interface and open-source code across multiple platforms for Zisland Explorer, which is available at http://cefg.uestc.edu.cn/Zisland_Explorer/ or http://tubic.tju.edu.cn/Zisland_Explorer/.
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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.