ArticleNucleic acids research2016
Finding approximate gene clusters with Gecko 3.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 33 citations in OpenAlex.
- Generalized Gene Cluster Detection Using CLOCI.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Quantifying Hierarchical Conflicts in Homology Statements.Journal of molecular evolution · 2025Article
- De novo discovery of conserved gene clusters in microbial genomes with Spacedust.Nature methods · 2025Article
- CLOCI: unveiling cryptic fungal gene clusters with generalized detection.Nucleic acids research · 2024Article
- New algorithms for structure informed genome rearrangement.Algorithms for molecular biology : AMB · 2023Article
- SYNPHONI: scale-free and phylogeny-aware reconstruction of synteny conservation and transformation across animal genomes.Bioinformatics (Oxford, England) · 2022Article
- Core circadian clock and light signaling genes brought into genetic linkage across the green lineage.Plant physiology · 2022Article
- Approximate search for known gene clusters in new genomes using PQ-trees.Algorithms for molecular biology : AMB · 2021Article
- Discovery of multi-operon colinear syntenic blocks in microbial genomes.Bioinformatics (Oxford, England) · 2020Article
- Analysis of local genome rearrangement improves resolution of ancestral genomic maps in plants.BMC genomics · 2020Article
- EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes.Bioinformatics (Oxford, England) · 2020Article
- Comparative genome characterization of the periodontal pathogen Tannerella forsythia.BMC genomics · 2020Article
- Evolutionary and functional patterns of shared gene neighbourhood in fungi.Nature microbiology · 2019Article
- GraphTeams: a method for discovering spatial gene clusters in Hi-C sequencing data.BMC genomics · 2018Article
- Modules of co-occurrence in the cyanobacterial pan-genome reveal functional associations between groups of ortholog genes.PLoS genetics · 2018Article
- LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis.Journal of integrative bioinformatics · 2017Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding gene clusters in hundreds of genomes. Existing tools are often restricted to few (in many cases, only two) genomes, and often make restrictive assumptions such as short perfect conservation, conserved gene order or monophyletic gene clusters. We present Gecko 3, an open-source software for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphical user interface. The underlying gene cluster model is intuitive, can cope with low degrees of conservation as well as misannotations and is complemented by a sound statistical evaluation. To evaluate the biological benefit of Gecko 3 and to exemplify our method, we search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a reference. We confirm detected gene clusters reviewing the literature and comparing them to a database of operons; we detect two novel clusters, which were confirmed by publicly available experimental RNA-Seq data. The computational analysis is carried out on a laptop computer in <40 min.
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