A CNV detection algorithm based on statistical analysis of the aligned reads |
Hong, Sang-Kyoon
(한림대학교 컴퓨터공학과)
Hong, Dong-Wan (한림대학교 바이오메디컬학과) Yoon, Jee-Hee (한림대학교 컴퓨터공학과) Kim, Baek-Sop (한림대학교 컴퓨터공학과) Park, Sang-Hyun (연세대학교 컴퓨터과학과) |
1 | F. S. Robert, "The Race for the $1000 Genome," SCIENCE, Vol.311, pp.1544-1546, 2006. DOI ScienceOn |
2 | R. Redon, et al, "Global variation in copy number in the human genome," Nature, Vol.444, pp.444-454, 2006. DOI ScienceOn |
3 | A. J. Iafrate, L. Feuk, M. N. Rivera, M. L. Listewnik, P. K. Donahoe, Y. Qi, S. W. Scherer, and C. Lee, "Detection of large-scale variation in the human genome," Nat. Genet., Vol.36, pp.949-951, 2004. DOI ScienceOn |
4 | http://maq.sourceforge.net |
5 | http://rulai.cshl.edu/rmap |
6 | http://brainarray.mbni.med.umich. edu/Brainarray/SequenceAlignment/AQUESA |
7 | 홍상균, 홍동완, 윤지희, 김종일. “Short read 서열정렬에 의한 CNV 영역 추출,” In proceedings of KDBC 2008, pp.297-305, 2008. |
8 | 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," Nat. Genet., Vol.37, No.7, pp.727-732, 2005. DOI ScienceOn |
9 | R. E. Mills, C. T. Luttig, C. E. Larkins, A. Beauchamp, C. Tsui, W. S. Pittard, and S. E. Devine, "An initial map of insertion and deletion (INDEL) variation in the human genome," Genome Res., Vol.16, pp.1182–1190, 2006. DOI ScienceOn |
10 | S. W. Schrer, C. Lee, E. Birney, D. M. Altshuler, E. E. Eichler, N. P. Carter, M. E. Hurles, and L. Feuk, "Challenges and standards in integrating surveys of structural variation," Nat. Genet., Vol.39, No.7, S7-S15, 2007. DOI ScienceOn |
11 | http://www.cbcb.umd.edu/software/RepeatFinder |
12 | R. L. Warren, G. G. Sutton, S. J. Jones, and R. A. Holt, "Assembling millions of short DNA sequences using SSAKE," Bioinformatics Vol.23, No.4, pp.500-501, 2007. DOI ScienceOn |
13 | J. C. Dohm, C. Lottaz, T. Borodina, and H. Himmelbauer, "SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing," Genome Res. Vol.17, No.11, pp.1697-1706, 2007 DOI ScienceOn |
14 | http://www.illumina.com |
15 | R. Li, et al, "SOAP: short oligonucleotide alignment program.," Bioinformatics Vol.24, No.5, pp.713-714, 2008. DOI ScienceOn |
16 | P. Weiner, "Linear Pattern Matching Algorithms," Proc. 14th IEEE Annual Symp. on Switching and Automata Theory, pp.1-11, 1973. DOI |
17 | W. W. Daniel, "Biostatistics (8th ed.)," Wiley, 2005. |
18 | U. Manber and G.e Myers, "Suffix arrays: a new method for on-line string searches," SIAM Journal on Computing, Vol.22, Issue 5, pp.935-948, 1993. DOI ScienceOn |
19 | S. W. Schrer, C. Lee, E. Birney, D. M. Altshuler, E. E. Eichler, N. P. Carter, M. E. Hurles, and L. Feuk, "Challenges and standards in integrating surveys of structural variation," Nat. Genet., Vol.39, No.7, S7-S15, 2007. DOI ScienceOn |
20 | S. Altschul, T. Madden, A. Schaffer, J. Zhang, W. Miller, and D. Lipman, "Gapped BLAST and PSI-BLAST: A New Generation of Protein Data-base Search Programs," Nucleic Acids Research, Vol.25 No.17 pp.3389-3402, 1997. DOI |
21 | http://projects.tcag.ca/variation |
22 | S. Tada, R. Hankins, and J. Patel, "Practical Suffix Tree Construction," In Proceedings of the 30th VLDB Conference, pp.36-47, 2004. |
23 | W. J. Kent, "BLAT - The Blast - Like Alignment Tool," Genome Research, Vol.12, No.4, pp.656-664, 2002. DOI |
24 | J. Sebat, B. Lakshmi, J. Troge, J. Alexander, J. Young, P. Lundin, S. Månér, H. Massa, M. Walker, M. Chi, N. Navin, R. Lucito, J. Healy, J. Hicks, K. Ye, A. Reiner, T. C. Gillian, B. Trask, N. Patterson, A. Zetterberg, and M. Wigler, "Large-Scale Copy Number Polymorphism in the Human Genome," Science, Vol.305, pp.525-528, 2004. DOI ScienceOn |
25 | R. Khaja, J. Zhang, J. R. MacDonal, H. Yongshu, M. J. Joseph-George, J. Wei, M. A. Rafiq, C. Qian, Shago M., L. Pantano, H. Aburatani, K. Jones, R. Redon, M. Hurles, L. Armengol, X. Estivill, R. J. Mural, C. Lee, S. W. Scherer, and L. Feuk, "Genome assembly comparison identifies structural variants in the human genome," Nat. Genet., Vol.38, No.12, pp.1413-1418, 2006. DOI ScienceOn |
26 | W. R. Jeck, J. A. Reinhardt, D. A. Baltrus, M. T. Hickenbotham, V. Magrini, E. R. Mardis, J. L. Dangl, and C. D. Jones, "Extending assembly of short DNA sequences to handle error," Bioinformatics Vol.23, No.21, pp.2942-2944, 2007. DOI ScienceOn |
27 | D. L. Wheeler, C. Chappey, A. E. Lash, D. D. Leipe, T. L. Madden, G. D. Schuler, T. A. Tatusova and B. A. Rapp, "Database resources of the National Center for Biotechnology Information," Nucleic Acids Research, Vol.28 No.1 pp.10-14, 2000. DOI |