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Issue No.05 - Sept.-Oct. (2013 vol.10)
pp: 1091-1097
Reginaldo M. Kuroshu , Inst. de Cienc. e Tecnol., Univ. Fed. de Sao Paulo, Sao Josedos Campos, Brazil
Simultaneously sequencing multiple clones using second-generation sequencers can speed up many essential clone-based sequencing methods. However, in applications such as fosmid clone sequencing and full-length cDNA sequencing, it is important to create pools of clones that do not overlap on the genome for the identification of structural variations and alternatively spliced transcripts, respectively. We define the nonoverlapping clone pooling problem and provide practical solutions based on optimal graph coloring and bin-packing algorithms with constant absolute worst-case ratios, and further extend them to cope with repetitive mappings. Using theoretical analysis and experiments, we also show that the proposed methods are applicable.
Cloning, Bioinformatics, Sequential analysis, Genomics, Approximation methods, Approximation algorithms,nonoverlapping clone pooling, Bin-packing, graph coloring, next-generation sequencing
Reginaldo M. Kuroshu, "Nonoverlapping Clone Pooling for High-Throughput Sequencing", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, no. 5, pp. 1091-1097, Sept.-Oct. 2013, doi:10.1109/TCBB.2013.83
[1] E.G. CoffmanJr., M.R. Garey, and D.S. Johnson, "Approximation Algorithms for Bin Packing," A Survey Approximation Algorithms for NP-Hard Problems, pp. 46-93, PWS Publishing, 1997.
[2] U.I. Gupta, D.T. Lee, and J.Y.T Leung, "Efficient Algorithms for Interval Graphs and Circular-Arc Graphs," Networks, vol. 12, pp. 459-467, 1982.
[3] I. Hajirasouliha, F. Hormozdiari, S.C. Sahinalp, and I. Birol, "Optimal Pooling for Genome Re-Sequencing with Ultra-High-Throughput Short-Read Technologies," Bioinformatics, vol. 24, pp. i32-i40, 2008.
[4] K. Jansen, "An Approximation Scheme for Bin Packing with Conflicts," J. Combinatorial Optimization, vol. 3, pp. 363-377, 1999.
[5] K. Jansen and S. Öhring, "Approximation Algorithms for Time Constrained Scheduling," Information and Computation, vol. 132, pp. 85-108, 1997.
[6] T.R. Jensen and B. Toft, Graph Coloring Problems. Wiley Interscience, 1995.
[7] R.M. Karp, "Reducibility among Combinatorial Problems," Complexity of Computer Computations, pp. 85-103, Plenum, 1972.
[8] J.M. Kidd, G.M. Cooper, W.F. Donahue, H.S. Hayden, N. Sampas, T. Graves, N. Hansen, B. Teague, C. Alkan, F. Antonacci, E. Haugen, T. Zerr, N.A. Yamada, P. Tsang, T.L. Newman, E. Tuzun, Z. Cheng, H.M. Ebling, N. Tusneem, R. David, W. Gillett, K.A. Phelps, M. Weaver, D. Saranga, A. Brand, W. Tao, E. Gustafson, K. McKernan, L. Chen, M. Malig, J.D. Smith, J.M. Korn, S.A. McCarroll, D.A. Altshuler, D.A. Peiffer, M. Dorschner, J. Stamatoyannopoulos, D. Schwartz, D.A. Nickerson, J.C. Mullikin, R.K. Wilson, L. Bruhn, M.V. Olson, R. Kaul, D.R. Smith, and E.E. Eichler, "Mapping and Sequencing of Structural Variation from Eight Human Genomes," Nature, vol. 453, pp. 56-64, 2008.
[9] J.M. Kidd, T. Graves, T.L. Newman, R. Fulton, H.S. Hayden, M. Malig, J. Kallicki, R. Kaul, R.K. Wilson, and E.E. Eichler, "A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms," Cell, vol. 143, pp. 837-847, 2010.
[10] J.O. Kitzman, A.P. Mackenzie, A. Adey, J.B. Hiatt, R.P. Patwardhan, P.H. Sudmant, S.B. Ng, C. Alkan, R. Qiu, E.E. Eichler, and J. Shendure, "Haplotype-Resolved Genome Sequencing of a Gujarati Indian Individual," Nature Biotechnology, vol. 29, pp. 59-63, 2011.
[11] R.M. Kuroshu, J. Watanabe, S. Sugano, S. Morishita, Y. Suzuki, and M. Kasahara, "Cost-Effective Sequencing of Full-Length cDNA Clones Powered by a De Novo-Reference Hybrid Assembly," PLoS One, vol. 5, article e10517, 2010.
[12] K. Maruyama and S. Sugano, "Oligo-Capping: A Simple Method to Replace the Cap Structure of Eukaryotic mRNAs with Oligoribonucleotides," Gene, vol. 138, pp. 171-174, 1994.
[13] D. Simchi-Levi, "New Worst-Case Results for the Bin-Packing Problem," Naval Research Logistics, vol. 41, pp. 579-585, 1994.
[14] Y. Suzuki, K. Yoshitomo Nakagawa, K. Maruyama, A. Suyama, and S. Sugano, "Construction and Characterization of a Full Length-Enriched and a 5'-End-Enriched cDNA Library," Gene, vol. 200, pp. 149-156, 1997.
[15] E. Tuzun, A.J. Sharp, J.A. Bailey, R. Kaul, V.A. Morrison, L.M. Pertz, E. Haugen, H. Hayden, D. Albertson, D. Pinkel, M.V. Olson, and E.E. Eichler, "Fine-Scale Structural Variation of the Human Genome," Nature Genetics, vol. 37, pp. 727-732, 2005.
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