A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Russell, David J ^a   Way, Samuel F ^a   Benson, Andrew K ^a   Sayood, Khalid ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SEQUENCES; CPU EXECUTION TIME; GRAMMAR-BASED DISTANCES; SEQUENCE CLUSTERING; SEQUENCE CLUSTERING ALGORITHMS; STATISTICAL ACCURACY; STATISTICAL CLUSTERING; VALIDATION RESULTS;

CLUSTERING ALGORITHMS;

RNA 16S;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

ALGORITHMS; BASE SEQUENCE; CLUSTER ANALYSIS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA;

EID: 78650145196     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-601     Document Type: Article

References (26)

1. Holm L, Sander C. Removing Near-Neighbour Redundancy from Large Protein Sequence Collections. Bioinformatics 1998, 14(5):423-429. 10.1093/bioinformatics/14.5.423, 9682055.
2. Li W, Jaroszewski L, Godzik A. Clustering of Highly Homologous Sequences to Reduce the Size of Large Protein Databases. Bioinformatics 2001, 17(3):282-283. 10.1093/bioinformatics/17.3.282, 11294794.
3. Li W, Jaroszewski L, Godzik A. Tolerating some Redundancy Significantly Speeds up Clustering of Large Protein Databases. Bioinformatics 2002, 18:77-82. 10.1093/bioinformatics/18.1.77, 11836214.
4. Parsons JD. Improved Tools for DNA Comparison and Clustering. Computer Applications in the Biosciences 1995, 11(6):603-613.
5. Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence Embedding for Fast Construction of Guide Trees for Multiple Sequence Alignment. Algorithms for Molecular Biology 2010, 5(21). 2893182, 20470396.
6. Li W, Godzik A. Cd-hit: a Fast Program for Clustering and Comparing Large Sets of Protein or Nucleotide Sequences. Bioinformatics 2006, 22(13):1658-1659. 10.1093/bioinformatics/btl158, 16731699.
7. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial Community Variation in Human Body Habitats Across Space and Time. Science 2009, 326:1694-1697. 10.1126/science.1177486, 19892944.
8. Edgar RC. Search and Clustering Orders of Magnitude Faster than BLAST. Bioinformatics 2010, 26(19):2460-2461. 10.1093/bioinformatics/btq461, 20709691.
9. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a New Generation of Protein Database Search Programs. Nucleic Acids Research 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
10. Lempel A, Ziv J. On the Complexity of Finite Sequences. IEEE Transactions on Information Theory 1976, 22:75-81.
11. Nevill-Manning CG, Witten IH. Compression and Explanation using Hierarchical Grammars. The Computer Journal 1997, 40(2/3):103-116.
12. Ziv J, Lempel A. A Universal Algorithm for Sequential Data Compression. IEEE Transactions on Information Theory 1977, 23(3):337-343.
13. Charikar M, Lehman E, Liu D, Panigrahy R, Prabhakaran M, Rasala A, Sahai A, Shelat A. Approximating the Smallest Grammar: Kolmogorov Complexity in Natural Models. STOC '02: Proceedings of the Thirty-Fourth Annual ACM Symposium on Theory of Computing 2002, 792-801. New York, NY, USA: ACM.
14. Ziv J, Lempel A. Compression of Individual Sequences via Variable-Rate Coding. IEEE Transactions on Information Theory 1978, 24(5):530-536.
15. Benedetto D, Caglioti E, Loreto V. Language Trees and Zipping. Physical Review Letters 2002, 88(4). 10.1103/PhysRevLett.88.048702, 11801178.
16. Otu HH, Sayood K. A New Sequence Distance Measure for Phylogenetic Tree Construction. Bioinformatics 2003, 19(16):2122-2130. 10.1093/bioinformatics/btg295, 14594718.
17. Russell DJ, Otu HH, Sayood K. Grammar-Based Distance in Progressive Multiple Sequence Alignment. BMC Bioinformatics 2008, 9(306). 2478692, 18616828.
18. Puglisi A, Benedetto D, Caglioti E, Loreto V, Vulpiani A. Data Compression and Learning in Time Sequences Analysis. Physica D: Nonlinear Phenomena 2003, 180:92-107.
19. Bastola DR, Otu HH, Doukas SE, Sayood K, Hinrichs SH, Iwen PC. Utilization of the Relative Complexity Measure to Construct a Phylogenetic Tree for Fungi. Mycological Research 2004, 108(2):117-125. 10.1017/S0953756203009079, 15119348.
20. Weiner P. Linear Pattern Matching Algorithms. 14th Annual Symposium on Switching and Automata Theory 1973, 1-11.
21. McCreight EM. A Space-Economical Suffix Tree Construction Algorithm. Journal of the ACM 1976, 23(2):262-272.
22. Ukkonen E. On-Line Construction of Suffix Trees. Algorithmica 1995, 14(3):249-260.
23. Wilbur WJ, Lipman DJ. Rapid Similarity Searches of Nucleic Acid and Protein Data Banks. Proceedings of the National Academy of Sciences of the United States of America 1983, 80:726-730. 10.1073/pnas.80.3.726, 393452, 6572363.
24. 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. 10.1093/nar/22.22.4673, 308517, 7984417.
25. Halkidi M, Batistakis Y, Vazirgiannis M. On Clustering Validation Techniques. Journal of Intelligent Information Systems 2001, 17(2-3):107-145.
26. Li W. Analysis and Comparison of Very Large Metagenomes with Fast Clustering and Functional Annotation. BMC Bioinformatics 2009, 10(359).