A multiple alignment approach for DNA sequences based on the maximum weighted path algorithms

Ruan Jian Xue Bao/Journal of Software

Volumn 18, Issue 2, 2007, Pages 185-195

  Huo, Hong Wei ^a   Xiao, Zhi Wei ^a  

^a XIDIAN UNIVERSITY   (China)

Author keywords

Consensus sequence; De Bruijn graph; Maximum weighted path; Multiple sequence alignment

Indexed keywords

DNA SEQUENCES; HIDDEN MARKOV MODELS;

COMPUTATION SPEED; COMPUTATIONAL TIME; CONSENSUS SEQUENCE; DE BRUIJN GRAPH; MAXIMUM WEIGHTED PATH; MULTIPLE SEQUENCE ALIGNMENT;

HEURISTIC ALGORITHMS;

EID: 34147205802     PISSN: 10009825     EISSN: None     Source Type: Journal    
DOI: 10.1360/jos180185     Document Type: Article

References (22)

1. Batzoglou S. The many faces of sequence alignment. Briefings in Bioinformatics, 2005, 6 (1): 6-22.
2. Needlman SB, Wunsch CD. A general method application to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 1970, 48 (3): 443-453.
3. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W. Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 1994, 22 (22): 4673-4680.
4. Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 2000, 302 (1): 205-217.
5. Barton GJ, Sternberg MJE. A strategy for the rapid multiple alignment of protein sequences. Journal of Molecular Biology, 1987, 198 (2): 327-337.
6. Katoh K, Misasa K, Kuma K, Miyata T. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research, 2002, 30 (14): 3059-3066.
7. Edgar RC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 2004, 32 (5): 1792-1797.
8. Van Walle I, Lasters I, Wyns L. Align-m - A new algorithm for multiple alignment of highly divergent sequences. Bioinformatics, 2004, 20 (9): 1428-1435.
9. Do CB, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple alignment of amino acid sequences. Genome Research, 2005, 15 (2): 330-340.
10. Lukashin AV, Engelbrecht J, Brunak S. Multiple alignment using simulated annealing: Branch point definition in human mRNA splicing. Nucleic Acids Research, 1992, 20 (10): 2511-2516.
11. Hernández-Guĺa M, Mulet R, Rodrĺguez-Pérez S. A new simulated annealing algorithm for the multiple sequence alignment problem: The approach of polymers in a random media. Physical Review E, 2005, 72 (3): 1-7.
12. Notredame C, Higgins DG. SAGA: Sequence alignment by genetic algorithm. Nucleic Acids Research, 1996, 24 (8): 1515-1524.
13. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics, 2002, 18 (3): 452-464.
14. Ye YZ, Godzik A. Multiple flexible structure alignment using partial order graphs. Bioinformatics, 2005, 21 (10): 2362-2369.
15. Raphael B, Zhi D, Tang H, Pevzner P. A novel method for multiple alignment of sequences with repeated and shuffled elements. Genome Research, 2004, 14 (11): 2336-2346.
16. Zhang Y, Waterman MS. An eulerian path approach to global multiple alignment for DNA sequences. Journal of Computational Biology, 2003, 10 (6): 803-819.
17. Idury RM, Waterman MS. A new algorithm for DNA sequence assembly. Computational Biology, 1995, 2 (2): 291-306.
18. Pevzner PA, Tang H, Waterman MS. An Eulerian path approach to DNA fragment assembly. Proc. of the National Academy of Sciences USA, 2001, 98 (17): 9748-9753.
19. Annexstein FS, De Bruijn G. Sequences: An efficient implementation. IEEE Trans. on Computers, 1997, 46 (2): 198-200.
20. Thompson JD, Plewniak F, Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acid Research, 1999, 27 (13): 2682-2690.
21. Goodrich MT, Write; Huo HW, Trans. Algorithm Design Foundations, Analysis and Internet Examples. Beijing: Posts and Telecommunications Press, 2006 (in Chinese).
22. Huo HW. Exercises and Solutions on Algorithms. Beijing: Higher Education Press, 2004.