CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes
Abstract Background The increasing availability of sequenced genomes has enabled comparative analyses of various organisms. Numerous tools and online platforms have been developed for this purpose, facilitating the identification of unique features within selected organisms. However, choosing the mo...
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BMC
2025-01-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06036-0 |
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| author | Gabriele Moro Rossano Atzeni Ali Al-Subhi Maria Giovanna Marche |
| author_facet | Gabriele Moro Rossano Atzeni Ali Al-Subhi Maria Giovanna Marche |
| author_sort | Gabriele Moro |
| collection | DOAJ |
| description | Abstract Background The increasing availability of sequenced genomes has enabled comparative analyses of various organisms. Numerous tools and online platforms have been developed for this purpose, facilitating the identification of unique features within selected organisms. However, choosing the most appropriate tools can be unclear during the initial stages of analysis, often requiring multiple attempts to match the specific characteristics of the data. Here, we introduce CompàreGenome, a command-line tool specifically designed for genomic diversity estimation analyses. Suitable for both prokaryotes and eukaryotes, this tool is particularly valuable in the early stages of studies when little information is available about the genetic differences or similarities among compared organisms. Results In all the tests conducted, CompàreGenome successfully identified specific genetic features of the selected organisms, detected the most conserved genes, pinpointed highly divergent ones, and functionally annotated these genes. This provided insights into biological processes, molecular functions, and cellular components associated with each gene. The tool also distinguished organisms at the strain level and quantified genetic distances using three distinct analytical methods. Conclusion CompàreGenome empowers users to explore genomic differences among organisms, translating technical outputs from various tools into actionable insights for biologists. While primarily tested on small microbial genomes, the tool has potential applications for larger genomes. CompàreGenome is implemented in Bash, R, and Python and is freely available under an LGPL-2.1 license. |
| format | Article |
| id | doaj-art-4982faec4b344efcbc4dbf0b743b4ac8 |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
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| series | BMC Bioinformatics |
| spelling | doaj-art-4982faec4b344efcbc4dbf0b743b4ac82025-01-19T12:40:56ZengBMCBMC Bioinformatics1471-21052025-01-0126111210.1186/s12859-025-06036-0CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotesGabriele Moro0Rossano Atzeni1Ali Al-Subhi2Maria Giovanna Marche3Technology Park of Sardinia, Bioecopest SrlCenter for Advanced Studies, Research and Development in SardiniaPlant Sciences Department, College of Agricultural and Marine Sciences, Sultanate Qaboos UniversityTechnology Park of Sardinia, Bioecopest SrlAbstract Background The increasing availability of sequenced genomes has enabled comparative analyses of various organisms. Numerous tools and online platforms have been developed for this purpose, facilitating the identification of unique features within selected organisms. However, choosing the most appropriate tools can be unclear during the initial stages of analysis, often requiring multiple attempts to match the specific characteristics of the data. Here, we introduce CompàreGenome, a command-line tool specifically designed for genomic diversity estimation analyses. Suitable for both prokaryotes and eukaryotes, this tool is particularly valuable in the early stages of studies when little information is available about the genetic differences or similarities among compared organisms. Results In all the tests conducted, CompàreGenome successfully identified specific genetic features of the selected organisms, detected the most conserved genes, pinpointed highly divergent ones, and functionally annotated these genes. This provided insights into biological processes, molecular functions, and cellular components associated with each gene. The tool also distinguished organisms at the strain level and quantified genetic distances using three distinct analytical methods. Conclusion CompàreGenome empowers users to explore genomic differences among organisms, translating technical outputs from various tools into actionable insights for biologists. While primarily tested on small microbial genomes, the tool has potential applications for larger genomes. CompàreGenome is implemented in Bash, R, and Python and is freely available under an LGPL-2.1 license.https://doi.org/10.1186/s12859-025-06036-0Comparative genomicsBioinformatics toolFunctional annotationMicroorganisms |
| spellingShingle | Gabriele Moro Rossano Atzeni Ali Al-Subhi Maria Giovanna Marche CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes BMC Bioinformatics Comparative genomics Bioinformatics tool Functional annotation Microorganisms |
| title | CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes |
| title_full | CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes |
| title_fullStr | CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes |
| title_full_unstemmed | CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes |
| title_short | CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes |
| title_sort | comparegenome a command line tool for genomic diversity estimation in prokaryotes and eukaryotes |
| topic | Comparative genomics Bioinformatics tool Functional annotation Microorganisms |
| url | https://doi.org/10.1186/s12859-025-06036-0 |
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