Reconstruction of ancestral gene orders using intermediate genomes
Feijão P (2015)
BMC Bioinformatics 16(Suppl 14): S3.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Einrichtung
Abstract / Bemerkung
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.
Stichworte
Ancestral Reconstruction;
Small Parsimony Problem;
Genome Rearrangement;
Double-Cut-and-Join
Erscheinungsjahr
2015
Zeitschriftentitel
BMC Bioinformatics
Band
16
Ausgabe
Suppl 14
Art.-Nr.
S3
ISSN
1471-2105
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2783101
Zitieren
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. doi:10.1186/1471-2105-16-S14-S3
Feijão, Pedro. 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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2019-09-06T09:18:34Z
MD5 Prüfsumme
4ff45e0069634f1e7b4f2cbaa3949fa7
Daten bereitgestellt von European Bioinformatics Institute (EBI)
7 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
A Median Solver and Phylogenetic Inference Based on Double-Cut-and-Join Sorting.
Xia R, Lin Y, Zhou J, Feng B, Tang J., J Comput Biol 25(3), 2018
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eSTGt: a programming and simulation environment for population dynamics.
Spiro A, Shapiro E., BMC Bioinformatics 17(1), 2016
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A novel procedure on next generation sequencing data analysis using text mining algorithm.
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Zhao W, Chen JJ, Perkins R, Wang Y, Liu Z, Hong H, Tong W, Zou W., BMC Bioinformatics 17(1), 2016
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Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies.
Velandia-Huerto CA, Berkemer SJ, Hoffmann A, Retzlaff N, Romero Marroquín LC, Hernández-Rosales M, Stadler PF, Bermúdez-Santana CI., BMC Genomics 17(1), 2016
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Alexeev N, Avdeyev P, Alekseyev MA., BMC Bioinformatics 17(suppl 14), 2016
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Rajaraman A, Ma J., BMC Bioinformatics 17(suppl 14), 2016
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Fast ancestral gene order reconstruction of genomes with unequal gene content.
Feijão P, Araujo E., BMC Bioinformatics 17(suppl 14), 2016
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