ArticleJournal of biosciences2010
INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms.
Article in Journal of biosciences, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 37 citations in OpenAlex.
- Genome-Based Evaluation of Safety and Probiotic Traits in Infant Feces-SourcedFoods (Basel, Switzerland) · 2026Article
- Current state and future prospects of Horizontal Gene Transfer detection.NAR genomics and bioinformatics · 2025Review
- Comprehensive genome sequence analysis ofFrontiers in microbiology · 2024Article
- Genomic Island Prediction via Chi-Square Test and Random Forest Algorithm.Computational and mathematical methods in medicine · 2021Article
- Genomic islands and the evolution of livestock-associated Staphylococcus aureus genomes.Bioscience reports · 2020Article
- New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements.Nucleic acids research · 2020Article
- 2SigFinder: the combined use of small-scale and large-scale statistical testing for genomic island detection from a single genome.BMC bioinformatics · 2020Article
- Microbial genomic island discovery, visualization and analysis.Briefings in bioinformatics · 2019Review
- 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
- Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.BMC genomics · 2018Article
- Comparative Analysis of Genomic Island Prediction Tools.Frontiers in genetics · 2018Article
- Insights into horizontal acquisition patterns of dormancy and reactivation regulon genes in mycobacterial species using a partitioning-based framework.Journal of biosciences · 2016Article
- Computational methods for predicting genomic islands in microbial genomes.Computational and structural biotechnology journal · 2016Review
- HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers.BMC genomics · 2014Article
- Identifying pathogenicity islands in bacterial pathogenomics using computational approaches.Pathogens (Basel, Switzerland) · 2014Review
- GIST: Genomic island suite of tools for predicting genomic islands in genomic sequences.Bioinformation · 2012Article
- EGID: an ensemble algorithm for improved genomic island detection in genomic sequences.Bioinformation · 2011Article
- Computational analysis of the ESX-1 region of Mycobacterium tuberculosis: insights into the mechanism of type VII secretion system.PloS one · 2011Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic islands (GIs) are regions in the genome which are believed to have been acquired via horizontal gene transfer events and are thus likely to be compositionally distinct from the rest of the genome. Majority of the genes located in a GI encode a particular function. Depending on the genes they encode, GIs can be classified into various categories, such as 'metabolic islands', 'symbiotic islands', 'resistance islands', 'pathogenicity islands', etc. The computational process for GI detection is known and many algorithms for the same are available. We present a new method termed as Improved N-mer based Detection of Genomic Islands Using Sequence-clustering (INDeGenIUS) for the identification of GIs. This method was applied to 400 completely sequenced species belonging to proteobacteria. Based on the genes encoded in the identified GIs, the GIs were grouped into 6 categories: metabolic islands, symbiotic islands, resistance islands, secretion islands, pathogenicity islands and motility islands. Several new islands of interest which had previously been missed out by earlier algorithms were picked up as GIs by INDeGenIUS. The present algorithm has potential application in the identification of functionally relevant GIs in the large number of genomes that are being sequenced. Investigation of the predicted GIs in pathogens may lead to identification of potential drug/vaccine candidates.
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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.