Abstract
Recently, the scaffold filling problem has attracted a lot of attention due to its potential applications in processing incomplete genomic data. However, almost all the current research assumes that a scaffold is given as an incomplete sequence (i.e., missing genes can be inserted anywhere in the incomplete sequence). This differs significantly from most of the real genomic dataset, where a scaffold is given as a sequence of contigs. We show in this paper that when a scaffold is given as a sequence of contigs, and when the genome contains no duplication of genes, the corresponding scaffold filling problem, with the objective being maximizing the number of adjacencies between the filled scaffold and a complete reference genome, is polynomially solvable.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bulteau, L., Carrieri, A.P., Dondi, R.: Fixed-parameter algorithms for scaffold filling. Theoret. Comput. Sci. 568, 72–83 (2015)
Chain, P.S., Grafham, D.V., Fulton, R.S., et al.: Genome project standards in a new era of sequencing. Science 326, 236–237 (2009)
Hopcroft, J., Karp, R.: An \(n^{5/2}\) algorithm for maximum matchings in bipartite graphs. SIAM J. Comput. 2(4), 225–231 (1973)
Jiang, H., Zheng, C., Sankoff, D., Zhu, B.: Scaffold filling under the breakpoint, related distances. IEEE/ACM Trans. Comput. Biol. Bioinform. 9(4), 1220–1229 (2012)
Jiang, H., Fan, C., Yang, B., Zhong, F., Zhu, D., Zhu, B.: Genomic scaffold filling revisited. In: Proceedings of the 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016), Tel Aviv, Israel, 27–29 June 2016, pp. 15:1–15:13 (2016)
Muñoz, A., Zheng, C., Zhu, Q., Albert, V., Rounsley, S., Sankoff, D.: Scaffold filling, contig fusion and gene order comparison. BMC Bioinform. 11, 304 (2010)
Sturtevant, A.: A crossover reducer in Drosophila melanogaster due to inversion of a section of the third chromosome. Biol. Zent. Bl. 46, 697–702 (1926)
Sturtevant, A., Dobzhansky, T.: Inversions in the third chromosome of wild races of drosophila pseudoobscura, and their use in the study of the history of the species. Proc. Nat. Acad. Sci. USA 22, 448–450 (1936)
Watterson, G., Ewens, W., Hall, T., Morgan, A.: The chromosome inversion problem. J. Theor. Biol. 99, 1–7 (1982)
Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340–3346 (2005)
Zhu, B.: Genomic scaffold filling: a progress report. In: Zhu, D., Bereg, S. (eds.) FAW 2016. LNCS, vol. 9711, pp. 8–16. Springer, Heidelberg (2016). doi:10.1007/978-3-319-39817-4_2
Acknowledgments
This research is partially supported by NSF of China under project 61628207, by the Foundation for Outstanding Young Scientists in Shandong Province (project no. BS2014DX017), by the Doctoral Foundation of Shandong Jianzhu University, and by the China Scholarship Council. We also thank anonymous reviewers for several useful comments.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing AG
About this paper
Cite this paper
Liu, N., Zou, P., Zhu, B. (2016). A Polynomial Time Solution for Permutation Scaffold Filling. In: Chan, TH., Li, M., Wang, L. (eds) Combinatorial Optimization and Applications. COCOA 2016. Lecture Notes in Computer Science(), vol 10043. Springer, Cham. https://doi.org/10.1007/978-3-319-48749-6_60
Download citation
DOI: https://doi.org/10.1007/978-3-319-48749-6_60
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-48748-9
Online ISBN: 978-3-319-48749-6
eBook Packages: Computer ScienceComputer Science (R0)