The Burrows-Wheeler similarity distribution between biological sequences based on Burrows-Wheeler transform

Journal of Theoretical Biology

Volumn 262, Issue 4, 2010, Pages 742-749

  Yang, Lianping ^a,b   Zhang, Xiangde ^b   Wang, Tianming ^a  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^b NORTHEASTERN UNIVERSITY   (China)

Author keywords

Distance measure; Entropy; Expectation; Phylogenetic tree

Indexed keywords

ALGORITHM; ENTROPY; PHYLOGENETICS;

ARTICLE; DNA SEQUENCE; ENTROPY; EXPECTATION; GENETIC DISTANCE; GENETIC SIMILARITY; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PRIORITY JOURNAL; SEQUENCE ALIGNMENT;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; DNA, MITOCHONDRIAL; DRUG DESIGN; ENTROPY; GENETIC TECHNIQUES; HUMANS; MEMBRANE PROTEINS; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; PHYLOGENY; PROTEIN FOLDING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TRANSFERRIN;

EID: 77649338338     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2009.10.033     Document Type: Article

References (59)

1. Althaus I.W., Chou J.J., Gonzales A.J., Diebel M.R., Chou K.C., Kezdy F.J., Romero D.L., Aristoff P.A., Tarpley W.G., Reusser F. Steady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201E. J. Biol. Chem. 1993, 268:6119-6124.
2. Althaus I.W., Gonzales A.J., Chou J.J., Diebel M.R., Chou K.C., Kezdy F.J., Romero D.L., Aristoff P.A., Tarpley W.G., Reusser F. The quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptase. J. Biol. Chem. 1993, 268:14875-14880.
3. Althaus I.W., Chou J.J., Gonzales A.J., Diebel M.R., Chou K.C., Kezdy F.J., Romero D.L., Aristoff P.A., Tarpley W.G., Reusser F. Kinetic studies with the nonnucleoside HIV-1 reverse transcriptase inhibitor U-88204E. Biochemistry 1993, 32:6548-6554.
4. Andraos J. Kinetic plasticity and the determination of product ratios for kinetic schemes leading to multiple products without rate laws: new methods based on directed graphs. Can. J. Chem. 2008, 86:342-357.
5. Blaisdell B. A measure of similarity of sets of sequences not requiring sequence alignment. Proc. Natl. Acad. Sci. 1986, 83:5155-5159.
6. Blaisdell B. Effectiveness of measures requiring and not requiring prior sequence alignment for estimating the dissimilarities of natural sequences. J. Mol. Evol. 1989, 29:526-537.
7. Burrows, M., Wheeler, D., 1994. A block sorting data compression algorithm. Digital SRC Research Report.
8. Chen X., Francia B., Li M. Shared information and program plagiarism detection. IEEE. Trans. Inf. Theory 2004, 50(7):1545-1551.
9. Cheng F., Shen J., Xu X., Luo X., Chen K., Shen X., Jiang H. Interaction models of a series of oxadiazole-substituted alpha-isopropoxy phenylpropanoic acids against PPARalpha and PPARgamma: molecular modeling and comparative molecular similarity indices analysis studies. Protein Pept. Lett. 2009, 16:150-162.
10. Chou K.C. Graphical rules in steady and non-steady enzyme kinetics. J. Biol. Chem. 1989, 264:12074-12079.
11. Chou K.C. Review: applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady state systems. Biophys. Chem. 1990, 35:1-24.
12. Chou K.C. A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. J. Biol. Chem. 1993, 268:16938-16948.
13. Chou K.C. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins Struct. Funct. Genet. 1995, 21:319-344.
14. Chou K.C. Review: prediction of HIV protease cleavage sites in proteins. Anal. Biochem. 1996, 233:1-14.
15. Chou K.C. Review: structural bioinformatics and its impact to biomedical science. Curr. Med. Chem. 2004, 11:2105-2134.
16. Chou K.C. Prediction of G-protein-coupled receptor classes. J. Proteome Res. 2005, 4:1413-1418.
17. Chou K.C., Zhang C.T. Diagrammatization of codon usage in 339 HIV proteins and its biological implication. AIDS Res. Hum. Retroviruses 1992, 8:1967-1976.
18. Chou K.C., Zhang C.T. Review: prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol. 1995, 30:275-349.
19. Chou K.C., Shen H.B. Signal-CF: a subsite-coupled and window-fusing approach for predicting signal peptides. Biochem. Biophys. Res. Commun. 2007, 357:633-640.
20. Chou K.C., Shen H.B. MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM. Biochem. Biophys. Res. Commun. 2007, 360:339-345.
21. Chou K.C., Shen H.B. Review: recent progresses in protein subcellular location prediction. Anal. Biochem. 2007, 370:1-16.
22. Chou K.C., Shen H.B. Cell-PLoc: a package of web-servers for predicting subcellular localization of proteins in various organisms. Nat. Protocols 2008, 3:153-162.
23. Chou K.C., Shen H.B. ProtIdent: a web server for identifying proteases and their types by fusing functional domain and sequential evolution information. Biochem. Biophys. Res. Commun. 2008, 376:321-325.
24. Chou K.C., Shen H.B. FoldRate: a web-server for predicting protein folding rates from primary sequence. Open Bioinformatics J. 2009, 3:31-50.
25. Chou K.C., Shen H.B. Review: recent advances in developing web-servers for predicting protein attributes. Nat. Sci. 2009, 2:63-92.
26. Chou K.C., Kezdy F.J., Reusser F. Review: steady-state inhibition kinetics of processive nucleic acid polymerases and nucleases. Anal. Biochem. 1994, 221:217-230.
27. Chou K.C., Zhang C.T., Elrod D.W. Do antisense proteins exist?. J. Protein Chem. 1996, 15:59-61.
28. Cilibrasi R., Vitányi P., de Wolf R. Algorithmic clustering of music based on string compression. Comput. Music. J. 2004, 28(4):49-67.
29. Crochemore M., Dsarmnien J., Perrin D. A note on the Burrows-Wheeler transformation. Theor. Comput. Sci. 2005, 332:567-572.
30. Dai Q., Yang Y., Wang T. Markov model plus k-word distributions: a synergy that produces novel statistical measures for sequence comparison. Bioinformatics 2008, 24(20):2296-2302.
31. Ford M. Molecular evolution of transferrin: evidence for positive selection in salmonids. Mol. Biol. Evol. 2001, 18:639-647.
32. Helden J.V. Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics 2004, 20:399-406.
33. Jia C., Liu T., Zhang X., Fu H., Yang Q. Alignment-free comparison of protein sequences based on reduced amino acids alphabets. J. Biomol. Struct. Dyn. 2009, 26:763-770.
34. Kantorovitz M., Robinson G., Sinha S. A statistical method for alignment free comparison of regulatory sequences. Bioinformatics 2007, 23:i249-i255.
35. Li M., Badger J., Chen X., Kwong S., Kearney P., Zhang H. An information based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 2001, 17:149-154.
36. Li M., Chen X., Li X., Ma B., Vitányi P. The similarity metric. IEEE Trans. Inf. Theory 2004, 12(5):3250-3264.
37. Lin J. Divergence measures based on the Shannon entropy. IEEE Trans. Inf. Theory 1991, 37:145-151.
38. Liu L., Wang T. Novel characterization of the folding of proteins. Int. J. Quantum Chem. 2007, 107:1970-1974.
39. Mantaci S., Restivo A., Rosone G., Sciortino M. An extension of the Burrows Wheeler transform. Theor. Comput. Sci. 2007, 387:298-312.
40. Mantaci S., Restivo A., Sciortino M. Burrows-Wheeler transform and Sturmian words. Inf. Process. Lett. 2003, 86:241-246.
41. Mantaci S., Restivo A., Sciortino M. Distance measures for biological sequences: some recent approaches. Int. J. Approx. Reason. 2008, 47:1-18.
42. Myers D., Palmer G. Microcomputer tools for steady-state enzyme kinetics. Bioinformatics 1985, 1:105-110.
43. Nandy A., Ghosh A., Nandy P. Numerical characterization of protein sequences and application to voltage-gated sodium channel α subunit phylogeny. In Silico Biol. 2009, 9:77-88.
44. Otu H., Sayood K. A new sequence distance measure for phylogenetic tree construction. Bioinformatics 2003, 19(16):2122-2130.
45. Pham T. Spectral distortion measures for biological sequence comparisons and database searching. Pattern Recognition 2007, 40:516-529.
46. Pham T., Zuegg J. A probabilistic measure for alignment-free sequence comparison. Bioinformatics 2004, 20:3455-3461.
47. Qi X.Q., Wen J., Qi Z.H. New 3D graphical representation of DNA sequence based on dual nucleotides. J. Theor. Biol. 2007, 249:681-690.
48. Randić M. 2-D graphical representation of proteins based on physico-chemical properties of amino acids. Chem. Phys. Lett. 2007, 440:291-295.
49. Randić M., Butina D., Zupan J. Novel 2-d graphical representation of proteins. Chem. Phys. Lett. 2006, 419:528-532.
50. Shen H.B., Song J.N., Chou K.C. Prediction of protein folding rates from primary sequence by fusing multiple sequential features. J. Biomed. Sci. Eng. 2009, 2:136-143.
51. Vinga S., Almeida J. Alignment free sequence comparison a review. Bioinformatics 2003, 19(4):513-523.
52. Xiao X., Chou K.C. Digital coding of amino acids based on hydrophobic index. Protein Pept. Lett. 2007, 14:871-875.
53. Xiao X., Wang P., Chou K.C. GPCR-CA: a cellular automaton image approach for predicting G-protein-coupled receptor functional classes. J. Comput. Chem. 2009, 30:1414-1423.
54. Xiao X., Wang P., Chou K.C. Predicting protein quaternary structural attribute by hybridizing functional domain composition and pseudo amino acid composition. J. Appl. Crystallogr. 2009, 42:169-173.
55. Xiao X., Shao S., Ding Y., Huang Z., Chen X., Chou K.C. Using cellular automata to generate Image representation for biological sequences. Amino Acids 2005, 28:29-35.
56. Zhang C., Zhang R. S curve, a graphic representation of protein secondary structure sequence and its applications. Biopolymers 2000, 53:539-549.
57. Zhang C.T., Chou K.C. Analysis of codon usage in 1562 E. Coli protein coding sequences. J. Mol. Biol. 1994, 238:1-8.
58. Zhang S., Yang L., Wang T. Use of information discrepancy measure to compare protein secondary structures. J. Mol. Struct. Theochem 2009, 909:102-106.
59. Zhou G.P., Deng M.H. An extension of Chou's graphical rules for deriving enzyme kinetic equations to system involving parallel reaction pathways. Biochem. J. 1984, 222:169-176.