Multiple genome comparison based on overlap regions of pairwise local alignments

Jahn K, Sudek H, Stoye J (2012)
BMC Bioinformatics 13(Suppl. 19: Proc. of RECOMB-CG 2012): S7.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
Background Mancheron, Uricaru and Rivals (Nucleic Acids Res. 39:e101, 2011) recently introduced a new approach in the context of multiple genome comparison that allows to detect regions of strong overlaps in a set of pairwise local alignments between several reference genomes and one target genome. Such overlap regions are an important source of information in genome annotation. Results In this paper we introduce a series of algorithms that improve over the approach of Mancheron et al., both in terms of computational complexity and in practical runtime. We also extend the problem definition such that overlaps to different reference genomes can be rated differently and regions overlapping only a subset of the reference genomes are detected.
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Zeitschriftentitel
BMC Bioinformatics
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13
Zeitschriftennummer
Suppl. 19: Proc. of RECOMB-CG 2012
Seite
S7
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Jahn K, Sudek H, Stoye J. Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinformatics. 2012;13(Suppl. 19: Proc. of RECOMB-CG 2012):S7.
Jahn, K., Sudek, H., & Stoye, J. (2012). Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinformatics, 13(Suppl. 19: Proc. of RECOMB-CG 2012), S7. doi:10.1186/1471-2105-13-S19-S7
Jahn, K., Sudek, H., and Stoye, J. (2012). Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinformatics 13, S7.
Jahn, K., Sudek, H., & Stoye, J., 2012. Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinformatics, 13(Suppl. 19: Proc. of RECOMB-CG 2012), p S7.
K. Jahn, H. Sudek, and J. Stoye, “Multiple genome comparison based on overlap regions of pairwise local alignments”, BMC Bioinformatics, vol. 13, 2012, pp. S7.
Jahn, K., Sudek, H., Stoye, J.: Multiple genome comparison based on overlap regions of pairwise local alignments. BMC Bioinformatics. 13, S7 (2012).
Jahn, Katharina, Sudek, Henner, and Stoye, Jens. “Multiple genome comparison based on overlap regions of pairwise local alignments”. BMC Bioinformatics 13.Suppl. 19: Proc. of RECOMB-CG 2012 (2012): S7.
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2018-08-14T11:29:43Z

1 Zitation in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Distribution of Plasmids in Distinct Leptospira Pathogenic Species.
Wang Y, Zhuang X, Zhong Y, Zhang C, Zhang Y, Zeng L, Zhu Y, He P, Dong K, Pal U, Guo X, Qin J., PLoS Negl Trop Dis 9(11), 2015
PMID: 26555137

2 References

Daten bereitgestellt von Europe PubMed Central.

Mauve: multiple alignment of conserved genomic sequence with rearrangements.
Darling AC, Mau B, Blattner FR, Perna NT., Genome Res. 14(7), 2004
PMID: 15231754
An alternative approach to multiple genome comparison.
Mancheron A, Uricaru R, Rivals E., Nucleic Acids Res. 39(15), 2011
PMID: 21646341

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