An algorithm for DNA multiple sequence alignment based on center star method and keyword tree

Tien Tzu Hsueh Pao/Acta Electronica Sinica

Volumn 37, Issue 8, 2009, Pages 1746-1750

  Zou, Quan ^a   Guo, Mao Zu ^a   Wang, Xiao Kai ^a   Zhang, Tao Tao ^a  

^a HARBIN INSTITUTE OF TECHNOLOGY   (China)

Author keywords

Aho Corasick algorithm; Bioinformatics; Center star method; Keyword tree; Multiple sequence alignment

Indexed keywords

AHO-CORASICK ALGORITHM; CENTER STAR METHOD; EVOLUTIONARY TREE; IMPROVED METHODS; KEYWORD TREE; LARGE DATA; MULTIPLE SEQUENCE ALIGNMENT; MULTIPLE SEQUENCE ALIGNMENTS; SUB-STRINGS; TIME COMPLEXITY; TREE-BASED ALGORITHMS;

ALIGNMENT; BIOINFORMATICS; NUCLEIC ACIDS; SYSTEMS ENGINEERING;

ALGORITHMS;

EID: 70249148008     PISSN: 03722112     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (10)

1. L Wang, T Jiang. On the complexity of multiple sequence alignment [J]. Journal of Computational Biology, 1994, 1 (4): 337-34.
2. Robert C Edgar, Serafim Batzoglou. Muitiple sequence alignment [J]. Current opinion in structural biology. 2006, 16 (3): 368-373.
3. Notredame C, Higgins D. G. SAGA: Sequence alignment by genetic algorithm [J]. Nucleic Acids Research. 1996, 24 (8): 1515-1524.
4. Serafim Batzoglou. The many faces of sequence alignment [J]. Briefings in Bioinformatics. 2005, 6 (1): 6-22.
5. Aho A V, Corasick M J. Efficient string matching: An aid to bibliographic search [J]. Communications of ACM, 1975, 18 (6): 333-340.
6. D Gusfield. Algorithms on strings, trees and sequences: Computer science and computational biology [M]. Cambridge: Cambridge University Press. 1997.
7. Quan Zou, Maozu Guo, Yang liu, Taotao Zhang. An Improved Algorithm for Aligning DNA/RNA Sequences Quickly [A]. International Conference on Computational Intelligence and Security [C]. Harbin: IEEE Press, 2007. 825-828.
8. D Gusfield. Efficient methods for multiple sequence alignment with guaranteed error bounds [J]. Bulletin of Mathematical Biology. 1993, 55 (1): 141-154.
9. Brown J W. The Ribonuclease P database [J]. Nucleic Acids Research, 1999, 27 (1): 314.
10. A Rambaut. Estimating the rate of molecular evolution: Incorporating noncontemporaneous sequences into maximum likelihood phylogenies [J]. Bioinformatics, 2000, 16 (4): 395-399.