Reconstruction of ancestral gene orders using intermediate genomes

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

Download
OA
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Volltext vorhanden für diesen Nachweis
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.
Erscheinungsjahr
Zeitschriftentitel
BMC Bioinformatics
Band
16
Ausgabe
Suppl 14
Art.-Nr.
S3
ISSN
Finanzierungs-Informationen
Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
PUB-ID

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, 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.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2016-02-24T13:33:51Z

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
PMID: 29035570
eSTGt: a programming and simulation environment for population dynamics.
Spiro A, Shapiro E., BMC Bioinformatics 17(1), 2016
PMID: 27117841
A novel procedure on next generation sequencing data analysis using text mining algorithm.
Zhao W, Chen JJ, Perkins R, Wang Y, Liu Z, Hong H, Tong W, Zou W., BMC Bioinformatics 17(1), 2016
PMID: 27177941
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
PMID: 27515907
Comparative genomics meets topology: a novel view on genome median and halving problems.
Alexeev N, Avdeyev P, Alekseyev MA., BMC Bioinformatics 17(suppl 14), 2016
PMID: 28185564
Fast ancestral gene order reconstruction of genomes with unequal gene content.
Feijão P, Araujo E., BMC Bioinformatics 17(suppl 14), 2016
PMID: 28185578

26 References

Daten bereitgestellt von Europe PubMed Central.

Multiple genome rearrangement and breakpoint phylogeny.
Sankoff D, Blanchette M., J. Comput. Biol. 5(3), 1998
PMID: 9773350
Efficient sorting of genomic permutations by translocation, inversion and block interchange.
Yancopoulos S, Attie O, Friedberg R., Bioinformatics 21(16), 2005
PMID: 15951307
A unifying view of genome rearrangements
AUTHOR UNKNOWN, 2006
Breakpoint graphs and ancestral genome reconstructions.
Alekseyev MA, Pevzner PA., Genome Res. 19(5), 2009
PMID: 19218533
On the PATHGROUPS approach to rapid small phylogeny.
Zheng C, Sankoff D., BMC Bioinformatics 12 Suppl 1(), 2011
PMID: 21342571
GASTS: Parsimony scoring under rearrangements
AUTHOR UNKNOWN, 2011
Rearrangement-based phylogeny using the Single-Cut-or-Join operation.
Biller P, Feijao P, Meidanis J., IEEE/ACM Trans Comput Biol Bioinform 10(1), 2013
PMID: 23702549
SCJ: a breakpoint-like distance that simplifies several rearrangement problems.
Feijao P, Meidanis J., IEEE/ACM Trans Comput Biol Bioinform 8(5), 2011
PMID: 21339538
Reconstructing contiguous regions of an ancestral genome.
Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W., Genome Res. 16(12), 2006
PMID: 16983148
ANGES: reconstructing ANcestral GEnomeS maps.
Jones BR, Rajaraman A, Tannier E, Chauve C., Bioinformatics 28(18), 2012
PMID: 22820205
MLGO: phylogeny reconstruction and ancestral inference from gene-order data.
Hu F, Lin Y, Tang J., BMC Bioinformatics 15(), 2014
PMID: 25376663
ProCARs: Progressive Reconstruction of Ancestral Gene Orders.
Perrin A, Varre JS, Blanquart S, Ouangraoua A., BMC Genomics 16 Suppl 5(), 2015
PMID: 26040958
The solution space of sorting by DCJ.
Braga MD, Stoye J., J. Comput. Biol. 17(9), 2010
PMID: 20874401
Multichromosomal median and halving problems under different genomic distances.
Tannier E, Zheng C, Sankoff D., BMC Bioinformatics 10(), 2009
PMID: 19386099
Combinatorial structure of genome rearrangements scenarios.
Ouangraoua A, Bergeron A., J. Comput. Biol. 17(9), 2010
PMID: 20874400
The On-Line Encyclopedia of Integer Sequences
AUTHOR UNKNOWN, 2010
An exact solver for the DCJ median problem.
Zhang M, Arndt W, Tang J., Pac Symp Biocomput (), 2009
PMID: 19209699
proTRAC--a software for probabilistic piRNA cluster detection, visualization and analysis.
Rosenkranz D, Zischler H., BMC Bioinformatics 13(), 2012
PMID: 22233380
Inversion-based genomic signatures.
Swenson KM, Moret BM., BMC Bioinformatics 10 Suppl 1(), 2009
PMID: 19208174
Maximum independent sets of commuting and noninterfering inversions.
Swenson KM, To Y, Tang J, Moret BM., BMC Bioinformatics 10 Suppl 1(), 2009
PMID: 19208163
Double cut and join with insertions and deletions.
Braga MD, Willing E, Stoye J., J. Comput. Biol. 18(9), 2011
PMID: 21899423
DCJ-Indel sorting revisited.
Compeau PE., Algorithms Mol Biol 8(1), 2013
PMID: 23452758

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 26451811
PubMed | Europe PMC

Suchen in

Google Scholar