De novo repeat classification and fragment assembly

Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB

Volumn 8, Issue , 2004, Pages 213-222

  Pevzner, Pavel A ^a   Tang, Haixu ^a   Tesler, Glenn ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Multiple Alignment; Repeat analysis; Sequence Assembly

Indexed keywords

ALGORITHMS; APPROXIMATION THEORY; COMPUTATIONAL METHODS; DNA; GENETIC ENGINEERING; GRAPH THEORY; PROBLEM SOLVING; TOPOLOGY;

FRAGMENT ASSEMBLY; MULTIPLE ALIGNMENT; REPEAT ANALYSIS; SEQUENCE ASSEMBLY;

BIOCHEMISTRY;

EID: 2442628273     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/974614.974643     Document Type: Conference Paper

References (35)

1. P. Agarwal and D. States. The Repeat Pattern Toolkit (RPT): analyzing the structure and evolution of the C. elegans genome. Proc. Int. Conf. Intel. Syst. Mol. Biol., 2:1-9, 1994.
2. S. Aparicio, J. Chapman, E. Stupka, N. Putnam, J. Chia, P. Dehal, A. Christoffels, S. Rash, S. Hoon, A. Smit, et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science, 297:1301-1310, 2002.
3. Z. Bao and S. Eddy. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res., 8:1269-1276, 2002.
4. S. Batzoglou, D. Jaffe, K. Stanley, J. Butler, S. Gnerre, E. Mauceli, B. Berger. J. Mesirov, and E. Lander. Arachne: a whole-genome shotgun assembler. Genome Res., 12:177-189, 2002.
5. J. Bedell, I. Korf, and W. Gish. MaskerAid: a performance enhancement to repeatmasker. Bioinformatics, 16:1040-1041, 2000.
6. S. Bocker. Sequencing from compomers: Using mass spectrometry for dna de-novo sequencing of 200+ nt. In 3rd Workshop on Algorithms in Bioinformatics, Budapest, September, Budapest, Hungary, September 2003. Lecture Notes in Computer Science.
7. G. Bourque, P. Pevzner, and G. Tesler. Reconstructing the Genomic Architecture of Ancestral Mammals: Lessons from Human, Mouse, and Rat Genomes. Genome Res., 2004. (In press.)
8. T. Cormen, C. Leiserson, and R. Rivest. Introduction to Algorithms. The MIT Press, 1989.
9. N. de Bruijn. A combinatorial problem. Koninklije Nedderlandse Academie van Wetenshappen Proc, A49:758-764, 1946.
10. A. Delcher, S. Kasif, R. Fleischmann, J. Peterson, O. White and S. Salzberg. Alignment of whole genomes. Nucleic Acids Research, 27:2369-2376, 1999.
11. P. Green. Documentation for PHRAP. http://www.genome.washington.edu/UWGC/ analysistools/phrap.htm, 1994.
12. S. Heber, M. Alekseyev, S. Sze, H. Tang, and P. Pevzner. Splicing graphs and EST assembly problem. Bioinformatics (Proceedings of ISMB 2002), 18:5181-188, 2002.
13. X. Huang. A contig assembly program based on sensitive detection of fragment overlaps. Genomics, 14:18-25, 1992.
14. X. Huang. An improved sequence assembly program. Genomics, 33:21-31, 1996.
15. R. Idury and M. Waterman. A new algorithm for DNA sequence assembly. Journal of Computational Biology, 2:291-306, 1995.
16. S. Kurtz, J. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, and R. Giegerich. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res., 29(22):4633-4642, 2001.
17. S. Kurtz, F. Ohlebusch, C. Schleiermacher, J. Stoye, and R. Giegerich. Computation and visualization of degenerate repeats in complete genomes. Proc. Int. Conf. Intel. Syst. Mol. Biol. 8:228-238, 2000.
18. C. Lee, C. Grasso, and M. Sharlow. Multiple sequence alignment using partial order graphs. Bioinformatics, 18:452-464, 2002.
19. B. Morgenstern, A. Dress, and T. Werner. Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl. Acad. Sci. USA, 93:12098-12103, 1996.
20. J. Mullikin and Z. Ning. The Phusion assembler. Genome Res., 13:81-90, 2003.
21. J. Munkres. Topology, Prentice Hall. 1999.
22. E. M. Myers. Toward simplifying and accurately formulating fragment assembly. Journal of Computational Biology. 2:275-290, 1995.
23. E. W. Myers, G. G. Sutton, A. L. Deicher, I. M. Dew. D. P. Fasulo, M. J. Flanigan, S. A. Kravitz, C. M. Mobarry, K. H. Reinert, K. A. Remington, et al. A whole-genome assembly of Drosophila. Science. 287:2196-2204, 2000.
24. I. Peer, N. Arbili, and R. Shamir. A computational method for resequencing long UNA targets by universal oligonucleotide arrays. Proc. Natl. Acad. Sci. USA, 99:15492-15496, 2002.
25. P. Pevzner. Z-tuple DNA sequencing: computer analysis. Journal of Biomolecular Structure and Dynamics, 7:63-73, 1989.
26. P. Pevzner and H. Tang. Fragment assembly with double-barreled data. Bioinformatics, 17:5225-3233, 2001.
27. P. Pevzner, H. Tang, and M. Waterman. An eulerian path approach to DNA fragment assembly. Proc. Natl. Acad. Sci. USA, 98:9748-9753, 2001.
28. M. Pop, D. Kosack, and S. Salzberg. Hierarchical scaffolding with Bambus. Genome Res., 14:149-159, 2004.
29. R. Shamir and D. Tsur. Large scale sequencing by hybridization. In Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB-01), pages 267-279, Montreal, Canada, April 2001. ACM Press.
30. V. Sharma, C. Chen, and H. Tang. Benchmarking of fragment assembly algorithms. 2003. (In preparation.)
31. S. Skiena. A Note on NP-completeness of the Maximum Subraphs with Large Girth Problem. 2002.
32. J. Thompson, D. Higgins, and T. Gibson. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22:4673-4680, 1994.
33. N. Volfovsky, B. Haas, and S. Salzberg, A clustering method for repeat analysis in DNA sequences. Genome Biology, 2:27 pages (electronic), 2001.
34. J. Wang, G. Wong, P. Ni, Y. Han, X. Huang, J. Zhang, C. Ye, Y. Zhang, J. Hu, K. Zhang, and X. Xu. RePS: a sequence assembler that masks exact repeats identified from the shotgun data. Genome Res., 12:824-831, 2002.
35. S. Yang. Comparison of genomic assemblers. Advances in Genome Biology and Technology, February 2002, Marco Island, Florida.