Genomic distance under gene substitutions

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

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
2011
Zeitschriftentitel
BMC Bioinformatics
Band
12
Ausgabe
Suppl 9: Proc. of RECOMB-CG 2011
Art.-Nr.
S8
eISSN
1471-2105
Page URI
https://pub.uni-bielefeld.de/record/2396509

Zitieren

Dias Vieira Braga M, Machado R, Ribeiro LC, Stoye J. Genomic distance under gene substitutions. BMC Bioinformatics. 2011;12(Suppl 9: Proc. of RECOMB-CG 2011): S8.
Dias Vieira Braga, M., 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
Dias Vieira Braga, M., Machado, R., Ribeiro, L. C., and Stoye, J. (2011). Genomic distance under gene substitutions. BMC Bioinformatics 12:S8.
Dias Vieira Braga, M., et al., 2011. Genomic distance under gene substitutions. BMC Bioinformatics, 12(Suppl 9: Proc. of RECOMB-CG 2011): S8.
M. Dias Vieira Braga, et al., “Genomic distance under gene substitutions”, BMC Bioinformatics, vol. 12, 2011, : S8.
Dias Vieira Braga, M., Machado, R., Ribeiro, L.C., Stoye, J.: Genomic distance under gene substitutions. BMC Bioinformatics. 12, : S8 (2011).
Dias Vieira Braga, Marília, 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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