ArticleBMC bioinformatics2015
Pan-Tetris: an interactive visualisation for Pan-genomes.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Article
- Pan-genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges.Current genomics · 2025Review
- Visualizing metagenomic and metatranscriptomic data: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Review
- FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments.Frontiers in genetics · 2020Article
- Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds.BMC microbiology · 2019Article
- Efficient merging of genome profile alignments.Bioinformatics (Oxford, England) · 2019Article
- PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes.BMC bioinformatics · 2018Article
- Computational pan-genomics: status, promises and challenges.Briefings in bioinformatics · 2018Review
- RPAN: rice pan-genome browser for ∼3000 rice genomes.Nucleic acids research · 2017Article
- Highlights from the 5th Symposium on Biological Data Visualization: Part 1.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLarge-scale genome projects have paved the way to microbial pan-genome analyses. Pan-genomes describe the union of all genes shared by all members of the species or taxon under investigation. They offer a framework to assess the genomic diversity of a given collection of individual genomes and moreover they help to consolidate gene predictions and annotations. The computation of pan-genomes is often a challenge, and many techniques that use a global alignment-independent approach run the risk of not separating paralogs from orthologs. Also alignment-based approaches which take the gene neighbourhood into account often need additional manual curation of the results. This is quite time consuming and so far there is no visualisation tool available that offers an interactive GUI for the pan-genome to support curating pan-genomic computations or annotations of orthologous genes.
resultsWe introduce Pan-Tetris, a Java based interactive software tool that provides a clearly structured and suitable way for the visual inspection of gene occurrences in a pan-genome table. The main features of Pan-Tetris are a standard coordinate based presentation of multiple genomes complemented by easy to use tools compensating for algorithmic weaknesses in the pan-genome generation workflow. We demonstrate an application of Pan-Tetris to the pan-genome of Staphylococcus aureus.
conclusionsPan-Tetris is currently the only interactive pan-genome visualisation tool. Pan-Tetris is available from http://bit.ly/1vVxYZT.
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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.