Genomic distance under gene substitutions

Braga MDV, Machado R, Ribeiro LC, Stoye J (2011)
BMC Bioinformatics 12(Suppl 9: Proc. of RECOMB-CG 2011): S8.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
Background: The distance between two genomes is often computed by comparing only the common markers between them. Some approaches are also able to deal with non-common markers, allowing the insertion or the deletion of such markers. In these models, a deletion and a subsequent insertion that occur at the same position of the genome count for two sorting steps. Results: Here we propose a new model that sorts non-common markers with substitutions, which are more powerful operations that comprehend insertions and deletions. A deletion and an insertion that occur at the same position of the genome can be modeled as a substitution, counting for a single sorting step. Conclusions: Comparing genomes with unequal content, but without duplicated markers, we give a linear time algorithm to compute the genomic distance considering substitutions and double-cut-and-join (DCJ) operations. This model provides a parsimonious genomic distance to handle genomes free of duplicated markers, that is in practice a lower bound to the real genomic distances. The method could also be used to refine orthology assignments, since in some cases a substitution could actually correspond to an unannotated orthology.
Erscheinungsjahr
Zeitschriftentitel
BMC Bioinformatics
Band
12
Zeitschriftennummer
Suppl 9: Proc. of RECOMB-CG 2011
Seite
S8
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PUB-ID

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Braga MDV, Machado R, Ribeiro LC, Stoye J. Genomic distance under gene substitutions. BMC Bioinformatics. 2011;12(Suppl 9: Proc. of RECOMB-CG 2011):S8.
Braga, M. D. V., Machado, R., Ribeiro, L. C., & Stoye, J. (2011). Genomic distance under gene substitutions. BMC Bioinformatics, 12(Suppl 9: Proc. of RECOMB-CG 2011), S8. doi:10.1186/1471-2105-12-S9-S8
Braga, M. D. V., Machado, R., Ribeiro, L. C., and Stoye, J. (2011). Genomic distance under gene substitutions. BMC Bioinformatics 12, S8.
Braga, M.D.V., et al., 2011. Genomic distance under gene substitutions. BMC Bioinformatics, 12(Suppl 9: Proc. of RECOMB-CG 2011), p S8.
M.D.V. Braga, et al., “Genomic distance under gene substitutions”, BMC Bioinformatics, vol. 12, 2011, pp. S8.
Braga, M.D.V., Machado, R., Ribeiro, L.C., Stoye, J.: Genomic distance under gene substitutions. BMC Bioinformatics. 12, S8 (2011).
Braga, Marília D. V., Machado, Raphael, Ribeiro, Leonardo C., and Stoye, Jens. “Genomic distance under gene substitutions”. BMC Bioinformatics 12.Suppl 9: Proc. of RECOMB-CG 2011 (2011): S8.
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2012-02-07T15:29:45Z

4 Zitationen in Europe PMC

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
Orthology detection combining clustering and synteny for very large datasets.
Lechner M, Hernandez-Rosales M, Doerr D, Wieseke N, Thévenin A, Stoye J, Hartmann RK, Prohaska SJ, Stadler PF., PLoS One 9(8), 2014
PMID: 25137074
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
On the weight of indels in genomic distances.
Braga MD, Machado R, Ribeiro LC, Stoye J., BMC Bioinformatics 12 Suppl 9(), 2011
PMID: 22151784

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Braga MD, Machado R, Ribeiro LC, Stoye J., BMC Bioinformatics 12 Suppl 9(), 2011
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