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EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements
Tom Hartmann1, Matthias Bernt2, Martin Middendorf3
1Swarm Intelligence and Complex Systems Group, Faculty of Mathematics and Computer Science, Leipzig University, Augustusplatz 10, Leipzig, D-04109, Germany. thartmann@informatik.uni-leipzig.de.
BMC Bioinformatics
|May 31, 2018
Summary
Understanding tandem duplication random loss (TDRL) in circular genomes requires analyzing all possible TDRL events. The EqualTDRL program facilitates this by computing and illustrating all TDRLs for gene order pairs, aiding evolutionary studies.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Studying unichromosomal circular genomes, like mitochondrial genomes, requires considering all potential tandem duplication random loss (TDRL) rearrangement events.
- Reconstructing a single TDRL event from initial and final gene orders can be ambiguous due to multiple possible rearrangement pathways.
Purpose of the Study:
- To present the EqualTDRL program for computing and illustrating the complete set of TDRLs between pairs of circular gene orders.
- To identify the minimum set of TDRLs based on the number of duplicated genes.
Main Methods:
- The EqualTDRL program analyzes pairs of circular gene orders that differ by a single TDRL event.
- It incorporates constraints such as conserved gene sequences and gene pairs flanking intergenic regions.
Main Results:
- EqualTDRL computes and visualizes the full spectrum of TDRL rearrangements for given circular genome pairs.
- The program can determine the minimal set of TDRLs, minimizing gene duplications.
Conclusions:
- EqualTDRL aids scientists in comprehensively studying TDRL events in mitochondrial genome evolution.
- The software is implemented in C++ with R (ggplot2) and is publicly available.
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