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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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Mapping Mammalian 3D Genome Interactions with Micro-C-XL

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Published on: November 3, 2023

Pan-Tetris: an interactive visualisation for Pan-genomes.

André Hennig, Jörg Bernhardt, Kay Nieselt

BMC Bioinformatics

|September 3, 2015

Summary

This summary is machine-generated.

This study introduces Pan-Tetris, an interactive software tool for visualizing microbial pan-genomes. It aids in curating gene predictions and annotations, addressing challenges in genomic diversity analysis.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Microbial pan-genome analysis is crucial for understanding species genomic diversity and consolidating gene predictions.
Current pan-genome computation methods face challenges in distinguishing orthologs from paralogs and often require time-consuming manual curation.
There is a lack of interactive visualization tools to support the curation of pan-genomic computations and orthologous gene annotations.

Purpose of the Study:

To introduce Pan-Tetris, an interactive software tool designed for the visual inspection of gene occurrences within microbial pan-genome tables.
To provide a user-friendly interface that compensates for algorithmic limitations in pan-genome generation workflows.
To facilitate the curation of pan-genomic data and orthologous gene annotations.

Main Methods:

Development of Pan-Tetris, a Java-based interactive software tool.
Implementation of a standard coordinate-based presentation for multiple genomes.
Inclusion of user-friendly tools to address weaknesses in pan-genome generation algorithms.

Main Results:

Pan-Tetris offers a structured visual inspection of gene occurrences in pan-genome tables.
The software effectively compensates for algorithmic limitations in pan-genome workflows.
Demonstrated application of Pan-Tetris to the pan-genome of Staphylococcus aureus.

Conclusions:

Pan-Tetris is the first interactive visualization tool specifically for pan-genomes.
The tool supports the curation of pan-genomic computations and orthologous gene annotations.
Pan-Tetris is available for download, promoting wider adoption in microbial genomics research.