Abstract
Reconstruct and quantify the RNA molecules in a cell at a given moment is an important problem in molecular biology that allows one to know which genes are being expressed and at which intensity level. Such problem is known as Transcriptome Reconstruction and Quantification Problem (TRQP). Although several approaches were already designed that solve the TRQP, none of them model it as a combinatorial optimization problem. In order to narrow this gap, we present here a new combinatorial optimization problem called Maximum Similarity Partitioning Problem (MSPP) that models the TRQP. In addition, we prove that the MSPP is NP-complete in the strong sense and present a greedy heuristic for it.
This work has been supported by FUNDECT-Brasil/MS (process number: 23/200, 500/2014. FUNDECT number: 185/2014).
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
Preview
Unable to display preview. Download preview PDF.
References
Li, J.J., Jiang, C.R., Brown, J.B., Huang, H., Bicke, P.J.: Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proceedings of the National Academy of Sciences 108(50), 19 867–19 872 (2011)
Schulz, M.H., Zerbino, D.R., Vingron, M., Birney, E.: Oases: robust de novo RNA-Seq assembly across the dynamic range of expression levels. Bioinformatics 28(8), 1086–1092 (2012)
Trapnell, C., Williams, B.A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M.J., Salzberg, S.L., Wold, B.J., Pachter, L.: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature biotechnology 28(5), 511–515 (2010)
Guttman, M., Garber, M., Levin, J.Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M.J., Gnirke, A., Nusbaum, C., et al.: Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature biotechnology 28(5), 503–510 (2010)
Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al.: Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature biotechnology 29(7), 644–652 (2011)
Li, W., Feng, J., Jiang, T.: IsoLasso: a LASSO regression approach to RNA-Seq based transcriptome assembly. Journal of Computational Biology 18(11), 1693–1707 (2011)
Mezlini, A.M., Smith, E.J., Fiume, M., Buske, O., Savich, G.L., Shah, S., Aparicio, S., Chiang, D.Y., Goldenberg, A., Brudno, M.: iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome research 23(3), 519–529 (2013)
Behr, J., Kahles, A., Zhong, Y., Sreedharan, V.T., Drewe, P., R atsch, G.: MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples. Bioinformatics 29(20), 2529–2538 (2013)
Martin, J., Bruno, V.M., Fang, Z., Meng, X., Blow, M., Zhang, T., Sherlock, G., Snyder, M., Wang, Z.: Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads. BMC genomics 11(1), 663 (2010)
de Lima, L. I. S.: O problema do alinhamento de segmentos: Master’s thesis, Universidade Federal de Mato Grosso do Sul, October (2013) (in portuguese)
Pevzner, P.: Computational molecular biology: an algorithmic approach. MIT press (2000)
Garey, M., Johnson, D.: Computers and Intractability: A Guide to the Theory of NP-Completeness. Series of books in the mathematical sciences. W.H. Freeman (1979)
Wang, Z., Gerstein, M., Snyder, M.: RNA-Seq: a revolutionary tool for transcriptomics. Nature Reviews Genetics 10(1), 57–63 (2009)
Griebel, T., Zacher, B., Ribeca, P., Raineri, E., Lacroix, V., Guigó, R., Sammeth, M.: Modelling and simulating generic RNA-Seq experiments with the flux simulator. Nucleic acids research 40(20), 10073–10083 (2012)
Lu, B., Zeng, Z., Shi, T.: Comparative study of de novo assembly and genome-guided assembly strategies for transcriptome reconstruction based on RNA-Seq. Science China Life Sciences 56(2), 143–155 (2013)
Martin, J.A., Wang, Z.: Next-generation transcriptome assembly. Nature Reviews Genetics 12(10), 671–682 (2011)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Zaccaron, A.Z., Adi, S.S., Higa, C.H.A., Araujo, E., Bluhm, B.H. (2015). The Maximum Similarity Partitioning Problem and its Application in the Transcriptome Reconstruction and Quantification Problem. In: Gervasi, O., et al. Computational Science and Its Applications -- ICCSA 2015. ICCSA 2015. Lecture Notes in Computer Science(), vol 9155. Springer, Cham. https://doi.org/10.1007/978-3-319-21404-7_19
Download citation
DOI: https://doi.org/10.1007/978-3-319-21404-7_19
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-21403-0
Online ISBN: 978-3-319-21404-7
eBook Packages: Computer ScienceComputer Science (R0)