Genomic Distance with High Indel Costs

da Silva PH, Machado R, Dantas S, Dias Vieira Braga M (2017)
IEEE/ACM Transactions on Computational Biology and Bioinformatics 14(3): 728-732.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
da Silva, Poly H.; Machado, Raphael; Dantas, Simone; Dias Vieira Braga, MaríliaUniBi
Einrichtung
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Technische Fakultät > AG Genominformatik
Abstract / Bemerkung
We determine complexity of computing the DCJ-indel distance, when DCJ and indel operations have distinct constant costs, by showing an exact formula that can be computed in linear time for any choice of (constant) costs for DCJ and indel operations. We additionally consider the problem of triangular inequality disruption and propose an algorithmically efficient correction on each member of the family of DCJ-indel.
Stichworte
Genome rearrangements; combinatorics; algorithms
Erscheinungsjahr
2017
Zeitschriftentitel
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Band
14
Ausgabe
3
Seite(n)
728-732
ISSN
1545-5963
eISSN
1557-9964
Page URI
https://pub.uni-bielefeld.de/record/2916552

Zitieren

da Silva PH, Machado R, Dantas S, Dias Vieira Braga M. Genomic Distance with High Indel Costs. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2017;14(3):728-732.
da Silva, P. H., Machado, R., Dantas, S., & Dias Vieira Braga, M. (2017). Genomic Distance with High Indel Costs. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14(3), 728-732. doi:10.1109/TCBB.2016.2555301
da Silva, Poly H., Machado, Raphael, Dantas, Simone, and Dias Vieira Braga, Marília. 2017. “Genomic Distance with High Indel Costs”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14 (3): 728-732.
da Silva, P. H., Machado, R., Dantas, S., and Dias Vieira Braga, M. (2017). Genomic Distance with High Indel Costs. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14, 728-732.
da Silva, P.H., et al., 2017. Genomic Distance with High Indel Costs. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14(3), p 728-732.
P.H. da Silva, et al., “Genomic Distance with High Indel Costs”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 14, 2017, pp. 728-732.
da Silva, P.H., Machado, R., Dantas, S., Dias Vieira Braga, M.: Genomic Distance with High Indel Costs. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 14, 728-732 (2017).
da Silva, Poly H., Machado, Raphael, Dantas, Simone, and Dias Vieira Braga, Marília. “Genomic Distance with High Indel Costs”. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14.3 (2017): 728-732.

12 References

Daten bereitgestellt von Europe PubMed Central.

Sorting Linear Genomes with Rearrangements and Indels.
Braga MD, Stoye J., IEEE/ACM Trans Comput Biol Bioinform 12(3), 2015
PMID: 26357261
The solution space of sorting by DCJ.
Braga MD, Stoye J., J. Comput. Biol. 17(9), 2010
PMID: 20874401

AUTHOR UNKNOWN, 0
DCJ-indel and DCJ-substitution distances with distinct operation costs.
da Silva PH, Machado R, Dantas S, Braga MD., Algorithms Mol Biol 8(1), 2013
PMID: 23879938
Efficient sorting of genomic permutations by translocation, inversion and block interchange.
Yancopoulos S, Attie O, Friedberg R., Bioinformatics 21(16), 2005
PMID: 15951307
Double cut and join with insertions and deletions.
Braga MD, Willing E, Stoye J., J. Comput. Biol. 18(9), 2011
PMID: 21899423
DCJ path formulation for genome transformations which include insertions, deletions, and duplications.
Yancopoulos S, Friedberg R., J. Comput. Biol. 16(10), 2009
PMID: 19803734
Sorting signed permutations by reversals and insertions/deletions of contiguous segments
el-mabrouk, Journal of Discrete Algorithms 1(), 2001

AUTHOR UNKNOWN, 0
On the weight of indels in genomic distances.
Braga MD, Machado R, Ribeiro LC, Stoye J., BMC Bioinformatics 12 Suppl 9(), 2011
PMID: 22151784

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 28113562
PubMed | Europe PMC

Suchen in

Google Scholar