Alignment free comparison: Similarity distribution between the DNA primary sequences based on the shortest absent word

Journal of Theoretical Biology

Volumn 295, Issue , 2012, Pages 125-131

  Yang, Lianping ^a   Zhang, Xiangde ^a   Zhu, Hegui ^a  

^a NORTHEASTERN UNIVERSITY   (China)

Author keywords

Eutherian orders; Hemoglobin sequence; Lexicographic order; Reversal complementary strand

Indexed keywords

DOUBLE STRANDED DNA;

DNA; EXPERIMENTAL STUDY; GENETIC ANALYSIS; HEMOGLOBIN; NUMERICAL MODEL; PHYLOGENETICS;

ALGORITHM; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; DNA STRAND; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; ANIMALS; DNA, MITOCHONDRIAL; ENTROPY; HUMANS; MODELS, GENETIC; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EUTHERIA;

EID: 83055163716     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2011.11.021     Document Type: Article

References (57)

1. Blaisdell B.E. A measure of the similarity of sets of sequences not requiring sequence alignment. Proc. Natl. Acad. Sci. USA 1986, 83:5155.
2. Cao Y., Janke A., Waddell P.J., Westerman M., Takenaka O., Murata S., Okada N., Paabo S., Hasegawa M. Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 1998, 47:307-322.
3. Chang G.S., Wang T.M. Phylogenetic analysis of protein sequences based on distribution of length about common substring. Protein J. 2011, 30:167-172.
4. Chou K.C. Insights from modeling three-dimensional structures of the human potassium and sodium channels. J. Proteome Res. 2004, 3:856-861.
5. Chou K.C. Some remarks on protein attribute prediction and pseudo amino acid composition. J. Theor. Biol. 2011, 273:236-247.
6. Chou K.C., Cai Y.D. Predicting protein-protein interactions from sequences in a hybridization space. J. Proteome Res. 2006, 5:316-322.
7. 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.
8. 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.
9. Chou K.C., Shen H.B. Recent advances in developing web-servers for predicting protein attributes. Nat. Sci. 2009, 1:63-92.
10. Chou K.C., Wu Z.C., Xiao X.A. iLoc-Euk: a multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins. PLoS One 2011, 6.
11. Chou K.C., Liu W.M., Maggiora G.M., Zhang C.T. Prediction and classification of domain structural classes. Proteins 1998, 31:97-103.
12. Ding Y.S., Zhang T.L., Gu Q., Zhao P.Y., Chou K.C. Using maximum entropy model to predict protein secondary structure with single sequence. Protein Pept. Lett. 2009, 16:552-560.
13. Domazet-Loso M., Haubold B. Alignment-free detection of local similarity among viral and bacterial genomes. Bioinformatics 2011, 27:1466-1472.
14. Du P., Cao S., Li Y. SubChlo: predicting protein subchloroplast locations with pseudo-amino acid composition and the evidence-theoretic K-nearest neighbor (ET-KNN) algorithm. J. Theor. Biol. 2009, 261:330-335.
15. Du P., He T., Li Y. Prediction of C-to-U RNA editing sites in higher plant mitochondria using only nucleotide sequence features. Biochem. Biophys. Res. Commun. 2007, 358:336-341.
16. Du P., Jia L., Li Y. CURE-Chloroplast: a chloroplast C-to-U RNA editing predictor for seed plants. BMC Bioinformatics 2009, 10:135.
17. Du P., Li T., Wang X. Recent progress in predicting protein sub-subcellular locations. Expert Rev. Proteomics 2011, 8:391-404.
18. Du Q.S., Huang R.B., Chou K.C. Advances in visual representation of molecular potentials. Expert Opin. Drug Discovery 2010, 5:513-527.
19. Garcia S.P., Pinho A.J., Rodrigues J., Bastos C.A.C., Ferreira P. Minimal absent words in prokaryotic and eukaryotic genomes. PLoS One 2011, 6.
20. Guyon F., Brochier-Armanet C., Guenoche A. Comparison of alignment free string distances for complete genome phylogeny. Adv. Data Anal. Classification 2009, 3:95-108.
21. Haubold B., Reed F.A., Pfaffelhuber P. Alignment-free estimation of nucleotide diversity. Bioinformatics 2011, 27:449-455.
22. Haubold B., Pfaffelhuber P., Domazet-Loso M., Wiehe T. Estimating mutation distances from unaligned genomes. J. Comput. Biol. 2009, 16:1487-1500.
23. He P.A., Zhang Y.P., Yao Y.H., Tang Y.F., Nan X.Y. The graphical representation of protein sequences based on the physicochemical properties and its applications. J. Comput. Chem. 2010, 31:2136-2142.
24. Huang T., Shi X.H., Wang P., He Z.S., Feng K.Y., Hu L.L., Kong X.Y., Li Y.X., Cai Y.D., Chou K.C. Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS One 2010, 5.
25. Jones D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 1999, 292:195-202.
26. Jun S.R., Sims G.E., Wu G.H.A., Kim S.H. Whole-proteome phylogeny of prokaryotes by feature frequency profiles: an alignment-free method with optimal feature resolution. Proc. Natl. Acad. Sci. USA 2010, 107:133-138.
27. Kantorovitz M.R., Robinson G.E., Sinha S. A statistical method for alignment-free comparison of regulatory sequences. Bioinformatics 2007, 23:I249-I255.
28. Li X., Liao B., Shu Y., Zeng Q., Luo J. Protein functional class prediction using global encoding of amino acid sequence. J. Theor. Biol. 2009, 261:290-293.
29. Li M., Badger J.H., Chen X., Kwong S., Kearney P., Zhang H.Y. An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics 2001, 17:149-154.
30. Liu Z., Liao B., Zhu W., Huang G. A 2D graphical representation of DNA sequence based on dual nucleotides and its application. Int. J. Quantum Chem. 2009, 109:948-958.
31. Liao B., Shan X.Z., Zhu W., Li R.F. Phylogenetic tree construction based on 2D graphical representation. Chem. Phys. Lett. 2006, 422:282-288.
32. Liao B., Wang T.M. 3-D graphical representation of DNA sequences and their numerical characterization. Theochem-J. Mol. Struct. 2004, 681:209-212.
33. Liao B., Liao B.Y., Sun X.M., Zeng Q.G. A Novel method for similarity analysis and protein sub-cellular localization prediction. Bioinformatics 2010, 26:2678-2683.
34. Otu H.H., Sayood K. A new sequence distance measure for phylogenetic tree construction. Bioinformatics 2003, 19:2122-2130.
35. Pham T.D., Zuegg J. A probabilistic measure for alignment-free sequence comparison. Bioinformatics 2004, 20:3455-3461.
36. Randic M., Vracko M., Lers N., Plavsic D. Novel 2-D graphical representation of DNA sequences and their numerical characterization. Chem. Phys. Lett. 2003, 368:1-6.
37. Randic M., Zupan J., Balaban A.T., Vikic-Topic D., Plavsic D. Graphical representation of proteins. Chem. Rev. 2011, 111:790-862.
38. Reinert G., Chew D., Sun F.Z., Waterman M.S. Alignment-free sequence comparison (I): statistics and power. J. Comput. Biol. 2009, 16:1615-1634.
39. Shen H.B., Chou K.C. Signal-3L: a 3-layer approach for predicting signal peptides. Biochem. Biophys. Res. Commun. 2007, 363:297-303.
40. Shen H.B., Chou K.C. HlVcleave: a web-server for predicting human immunodeficiency virus protease cleavage sites in proteins. Anal. Biochem. 2008, 375:388-390.
41. Shen H.B., Chou K.C. Identification of proteases and their types. Anal. Biochem. 2009, 385:153-160.
42. Shen H.B., Chou K.C. Predicting protein fold pattern with functional domain and sequential evolution information. J. Theor. Biol. 2009, 256:441-446.
43. Shen H.B., Yi D.L., Yao L.X., Yang J., Chou K.C. Knowledge-based computational intelligence development for predicting protein secondary structures from sequences. Expert Rev. Proteomics 2008, 5:653-662.
44. Sims G.E., Kim S.H. Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs). Proc. Natl. Acad. Sci. USA 2011, 108:8329-8334.
45. Sims G.E., Jun S.R., Wua G.A., Kim S.H. Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions. Proc. Natl. Acad. Sci. USA 2009, 106:2677-2682.
46. Ulitsky I., Burstein D., Tuller T., Chor B. The average common substring approach to phylogenomic reconstruction. J. Comput. Biol. 2006, 13:336-350.
47. Vinga S., Almeida J. Alignment-free sequence comparison-a review. Bioinformatics 2003, 19:513-523.
48. Wan L., Reinert G., Sun F.Z., Waterman M.S. Alignment-free sequence comparison (II): theoretical power of comparison statistics. J. Comput. Biol. 2010, 17:1467-1490.
49. Wang J.F., Wei D.Q., Chou K.C. Insights from investigating the interactions of adamantane-based drugs with the M2 proton channel from the H1N1 swine virus. Biochem. Biophys. Res. Commun. 2009, 388:413-417.
50. Wang T., Yang J., Shen H.B., Chou K.C. Predicting membrane protein types by the LLDA algorithm. Protein Pept. Lett. 2008, 15:915-921.
51. Wu T.J., Hsieh Y.C., Li L.A. Statistical measures of DNA sequence dissimilarity under Markov chain models of base composition. Biometrics 2001, 57:441-448.
52. Xiao X., Wang P., Chou K.C. Predicting the quaternary structure attribute of a protein by hybridizing functional domain composition and pseudo amino acid composition. J. Appl. Crystallogr. 2009, 42:169-173.
53. Xiao X., Wu Z.C., Chou K.C. A multi-label classifier for predicting the subcellular localization of gram-negative bacterial proteins with both single and multiple sites. PLoS One 2011, 6.
54. Xiao X.A., Wang P., Chou K.C. GPCR-2L: predicting G protein-coupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions. Mol. Biosyst. 2011, 7:911-919.
55. Yao Y.H., Nan X.Y., Wang T.M. A class of 2D graphical representations of RNA secondary structures and the analysis of similarity based on them. J. Comput. Chem. 2005, 26:1339-1346.
56. Yao Y.H., Dai Q., Li L., Nan X.Y., He P.A., Zhang Y.Z. Similarity/dissimilarity studies of protein sequences based on a new 2D graphical representation. J. Comput. Chem. 2010, 31:1045-1052.
57. Zhu W., Liao B., Li R. A method for constructing phylogenetic tree based on a dissimilarity matrix. Match-Commun. Math. Comput. Chem. 2010, 63:483-492.