Reconstruction of ancestral gene orders using intermediate genomes

Feijão P (2015)
BMC Bioinformatics 16(Suppl 14): S3.

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Journal Article | Published | English
Abstract
Background The problem of reconstructing ancestral genomes in a given phylogenetic tree arises in many different comparative genomics fields. Here, we focus on reconstructing the gene order of ancestral genomes, a problem that has been largely studied in the past 20 years, especially with the increasing availability of whole genome DNA sequences. There are two main approaches to this problem: event-based methods, that try to find the ancestral genomes that minimize the number of rearrangement events in the tree; and homology-based, that look for conserved structures, such as adjacent genes in the extant genomes, to build the ancestral genomes. Results We propose algorithms that use the concept of intermediate genomes, arising in optimal pairwise rearrangement scenarios. We show that intermediate genomes have combinatorial properties that make them easy to reconstruct, and develop fast algorithms with better reconstructed ancestral genomes than current event-based methods. The proposed framework is also designed to accept extra information, such as results from homology-based approaches, giving rise to combined algorithms with better results than the original methods.
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Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
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Feijão P. Reconstruction of ancestral gene orders using intermediate genomes. BMC Bioinformatics. 2015;16(Suppl 14): S3.
Feijão, P. (2015). Reconstruction of ancestral gene orders using intermediate genomes. BMC Bioinformatics, 16(Suppl 14): S3.
Feijão, P. (2015). Reconstruction of ancestral gene orders using intermediate genomes. BMC Bioinformatics 16:S3.
Feijão, P., 2015. Reconstruction of ancestral gene orders using intermediate genomes. BMC Bioinformatics, 16(Suppl 14): S3.
P. Feijão, “Reconstruction of ancestral gene orders using intermediate genomes”, BMC Bioinformatics, vol. 16, 2015, : S3.
Feijão, P.: Reconstruction of ancestral gene orders using intermediate genomes. BMC Bioinformatics. 16, : S3 (2015).
Feijão, Pedro. “Reconstruction of ancestral gene orders using intermediate genomes”. BMC Bioinformatics 16.Suppl 14 (2015): S3.
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PMID: 26451811
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