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Author: Nguyen Tien Thanh Department of Computer Science School of Computing National University of Singapore Date: 30 Aug 2012

This document provides an overview of a project on enhancing existing genome sorting algorithms. The objective is to allow all traditional genomic operations without restrictions in order to compute evolutionary distances more accurately. Existing algorithms like Pevzner's breakpoint graph and DCJ operator are described. The project plan involves evaluating these algorithms, enhancing them, and implementing the improved algorithms. Risks include not fully understanding the existing approaches and algorithms or managing time poorly.

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Nguyen Tien Thanh
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51 views18 pages

Author: Nguyen Tien Thanh Department of Computer Science School of Computing National University of Singapore Date: 30 Aug 2012

This document provides an overview of a project on enhancing existing genome sorting algorithms. The objective is to allow all traditional genomic operations without restrictions in order to compute evolutionary distances more accurately. Existing algorithms like Pevzner's breakpoint graph and DCJ operator are described. The project plan involves evaluating these algorithms, enhancing them, and implementing the improved algorithms. Risks include not fully understanding the existing approaches and algorithms or managing time poorly.

Uploaded by

Nguyen Tien Thanh
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Author: Nguyen Tien Thanh Department of Computer Science School of Computing National University of Singapore Date: 30 Aug 2012

Overview of the project Genome sorting problem Existing algorithms Evaluation of existing algorithms Project Plan - Project Schedule - Project Risks References Q&A

Objective
- To enhance existing genome sorting algorithms by allowing all traditional operations that can be performed and making no assumption on the two genomes.

Relevance - By applying no restriction, the evolutionary distances computed are hopefully closer to the real distances

Genome sorting problem - Given two genomes, rearrange one into another Restrictions

Limited operations Minimum distance

Examples:

Pevzner algorithm Breakpoint graph

DCJ operator invented by Yancopoulos A DCJ cuts a genome at 2 positions, then rejoins the cut ends in 2 new pairs Example: Reversal

Effect of DCJ on breakpoint graph

GRIMM (Genome Rearrangements in Man and Mouse) http://nbcr.sdsc.edu/GRIMM/grimm.cgi

MGRA - Multiple Genome Rearrangements and Ancestors (build a phylogenetic tree) http://mgra.bioinf.spbau.ru/

Use the cycle graph (an improved version of the breakpoint graph) with new ideas called T-bridge and X-bridge. Searching these bridges using a greedy algorithm can help determine the next optimal operation to perform on the genome.

Evaluate existing algorithms Enhancement of existing algorithms Implementation of improved algorithms

Project Risks Unable to fully understand the existing algorithms Unable to propose a better algorithm Unable to implement the improved algorithm Poor time management

How to tackle the risks - Regularly update progress. Consult supervisor and seniors. - Read paper selectively and try to get the main points. - Pick up necessary knowledge. - Use project management tools.

[1] M. Bader. Genome rearrangements with duplications. BMC Bioinformatics, 11(Suppl 1):S27, 2010. [2] F. Hao, J. Luan, and D. Zhu. Translocation-Deletions Distance Formula for Sorting Genomes. WRI World Congress on Computer Science and Information Engineering, 2009. [3] Neil C.Jones, and Pavel A. Pevzner, An introduction to bioinformatics algorithms, MIT Press, 2004. [4] Pavel A. Pevzner, Computational Molecular Biology An Algorithmic Approach, MIT Press, 2001. [5] Martin Bader, Sorting by Reversals, Block Interchanges, Tandem Duplications, and Deletions, 2009. [6] Martin Bader, Genome rearrangements with duplications, 2010.

THANK YOU!

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