Related Experiment Video
Updated: May 20, 2026
10:36
Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and
Ruchi Chaudhary1, J Gordon Burleigh, Oliver Eulenstein
1Department of Computer Science, Iowa State University, Ames, IA 50011, USA.
BMC Bioinformatics
|July 5, 2012
Summary
New algorithms efficiently correct gene tree errors by rearranging gene topologies, improving phylogenetic analyses and reconciliation cost estimates. This method enhances understanding of gene evolution and phylogenetics.
Area of Science:
- Computational Biology
- Evolutionary Biology
- Phylogenetics
Background:
- Gene tree-species tree reconciliation infers gene evolution patterns.
- Parsimony methods minimize gene duplication, loss, or deep coalescence events.
- Gene tree errors can significantly bias reconciliation results.
Purpose of the Study:
- Introduce efficient algorithms for gene tree rearrangement.
- Improve accuracy and speed in gene tree reconciliation.
- Provide a protocol for error correction in phylogenetic analyses.
Main Methods:
- Developed algorithms to search local Subtree Prune and Regraft (SPR) and Tree Bisection and Reconnection (TBR) neighborhoods.
- Algorithms achieve n-fold improvement for SPR and n2-fold for TBR searches.
- Implemented a protocol for gene rearrangement to improve reconciliation cost.
Main Results:
- Efficiently identify gene tree topologies with minimal evolutionary events.
- Algorithms significantly accelerate reconciliation searches.
- Demonstrated a fast error correction protocol for gene trees.
Conclusions:
- New algorithms offer a rapid solution for gene tree error.
- Method is model-agnostic regarding genome evolution processes.
- Algorithms enhance the credibility of phylogenetic analyses and reconciliation cost estimates.
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The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
02:46Genome Copying Errors
DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.
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