A singular value decomposition approach for improved taxonomic classification of biological sequences

BMC Genomics

Volumn 12, Issue SUPPL. 4, 2011, Pages

  Santos, Anderson R ^a   Santos, Marcos A ^a   Baumbach, Jan ^b   McCulloch, John A ^a   Oliveira, Guilherme C ^c   Silva, Artur ^d   Miyoshi, Anderson ^a   Azevedo, Vasco ^a  

^a FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

^b MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^c INSTITUTO OSWALDO CRUZ   (Brazil)

^d FEDERAL UNIVERSITY OF PARÁ   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; CLADISTICS; CLUSTER ANALYSIS; CONTROLLED STUDY; DATA ANALYSIS; GENOME; INFORMATION RETRIEVAL; INTERNET; MATHEMATICAL ANALYSIS; SINGULAR VALUE DECOMPOSITION; TAXONOMY; TIME; UNCERTAINTY; ALGORITHM; COMPUTER PROGRAM;

ALGORITHMS; CLUSTER ANALYSIS; INFORMATION STORAGE AND RETRIEVAL; SOFTWARE;

EID: 84255200947     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-S4-S11     Document Type: Article

References (21)

1. Golub G, Kahan W. Calculating the Singular Values and Pseudo-Inverse of a Matrix. Journal of the Society for Industrial and Applied Mathematics, Series B: Numerical Analysis 1965, 2:205-224.
2. Berry MW, Dumais ST, OBrien GW. Using Linear Algebra for Intelligent Information Retrieval. SIAM Review 1995, 37:573-595.
3. Élden L. Numerical linear algebra in data mining. Acta Numerica 2006, 15:327-384.
4. Élden L. Matrix Methods in Data Mining and Pattern Recognition. 2007, Society for Industrial and Applied Mathematics.
5. Fogolari F, Tessari S, Molinari H. Singular value decomposition analysis of protein sequence alignment score data. Proteins 2002, 46:161-170. 10.1002/prot.10032, 11807944.
6. Del-Castillo-Negrete D, Hirshman SP, Spong DA, DAzevedo EF. Compression of magnetohydrodynamic simulation data using singular value decomposition. Journal of Computational Physics 2007, 222:265-286.
7. Deerwester SC, Dumais ST, Furnas GW, Harshman RA, Landauer TK, Lochbaum KE, Streeter LA. Computer information retrieval using latent semantic structure. U. S. Patent: 4839853 1989,
8. Stuart GW, Moffett K, Leader JJ. A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes. Mol Biol Evol 2002, 19:554-562.
9. Vries JK, Liu X. Subfamily specific conservation profiles for proteins based on n-gram patterns. BMC Bioinformatics 2008, 9:72. 10.1186/1471-2105-9-72, 2267698, 18234090.
10. Ider YZ, Onart S. Algebraic reconstruction for 3D magnetic resonance-electrical impedance tomography (MREIT) using one component of magnetic flux density. Physiol Meas 2004, 25:281-294. 10.1088/0967-3334/25/1/032, 15005322.
11. Hartigan JA, W MA. Algorithm AS 136: A K-Means Clustering Algorithm. Journal of the Royal Statistical Society. Series C (Applied Statistics) 1979, 28:100-108.
12. Dempster AP, Laird NM, Rubin DB. Maximum Likelihood from Incomplete Data via the EM Algorithm. Journal of the Royal Statistical Society 1977, 39:1-38.
13. De Smet F, Mathys J, Marchal K, Thijs G, De Moor B, Moreau Y. Adaptive quality-based clustering of gene expression profiles. Bioinformatics 2002, 18:735-746. 10.1093/bioinformatics/18.5.735, 12050070.
14. Kaufman L, Rousseeuw P. Finding Groups in Data An Introduction to Cluster Analysis. 1990, Wiley Interscience.
15. Witten IH, Frank E, Hall MA. Data Mining: Practical Machine Learning Tools and Techniques. 2011, Morgan Kaufmann.
16. Team RDC. R: A Language and Environment for Statistical Computing. 2006,
17. Abeel T, de Peer YV, Saeys Y. Java-ML: A Machine Learning Library. Journal of Machine Learning Research 2009, 10:931-934.
18. Liu Q, Zhang Y, Xu Y, Ye X. Fuzzy kernel clustering of RNA secondary structure ensemble using a novel similarity metric. J Biomol Struct Dyn 2008, 25:685-696.
19. Vries JK, Munshi R, Tobi D, Klein-Seetharaman J, Benos PV, Bahar I. A sequence alignment-independent method for protein classification. Appl Bioinformatics 2004, 3:137-148. 10.2165/00822942-200403020-00008, 15693739.
20. Couto BRGM, Ladeira AP, Santos MA. Application of latent semantic indexing to evaluate the similarity of sets of sequences without multiple alignments character-by-character. Genet Mol Res 2007, 6:983-999.
21. Gordon AD, Vichi M. Partitions of Partitions. Journal of Classification 1998, 15:265-285.