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Journal article
Sorting by reversals, block interchanges, tandem duplications, and deletions
BMC bioinformatics, v 10 Suppl 1(1), pp S9-S9
30 Jan 2009
PMID: 19208182
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Finding sequences of evolutionary operations that transform one genome into another is a classic problem in comparative genomics. While most of the genome rearrangement algorithms assume that there is exactly one copy of each gene in both genomes, this does not reflect the biological reality very well--most of the studied genomes contain duplicated gene content, which has to be removed before applying those algorithms. However, dealing with unequal gene content is a very challenging task, and only few algorithms allow operations like duplications and deletions. Almost all of these algorithms restrict these operations to have a fixed size.
In this paper, we present a heuristic algorithm to sort an ancestral genome (with unique gene content) into a genome of a descendant (with arbitrary gene content) by reversals, block interchanges, tandem duplications, and deletions, where tandem duplications and deletions are of arbitrary size.
Experimental results show that our algorithm finds sorting sequences that are close to an optimal sorting sequence when the ancestor and the descendant are closely related. The quality of the results decreases when the genomes get more diverged or the genome size increases. Nevertheless, the calculated distances give a good approximation of the true evolutionary distances.
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Details
- Title
- Sorting by reversals, block interchanges, tandem duplications, and deletions
- Creators
- Martin Bader - University of UlmJun Liu - Neurobiology and Anatomy
- Publication Details
- BMC bioinformatics, v 10 Suppl 1(1), pp S9-S9
- Publisher
- Springer BMC
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Neurobiology and Anatomy
- Web of Science ID
- WOS:000265601900009
- Scopus ID
- 2-s2.0-65449117238
- Other Identifier
- 991019173706604721
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Data related to this publication, from InCites Benchmarking & Analytics tool:
- Web of Science research areas
- Biochemical Research Methods
- Biotechnology & Applied Microbiology
- Mathematical & Computational Biology