A measure of dna sequence dissimilarity based on free energy of nearest-neighbor interaction

Journal of Biomolecular Structure and Dynamics

Volumn 28, Issue 4, 2011, Pages 557-565

  Zhang, Yusen ^a   Chen, Wei ^a  

^a SHANDONG UNIVERSITY   (China)

Author keywords

Free energy; Nearest neighbor interaction; Selectivity; Sensitivity; Sequence comparison

Indexed keywords

ARTICLE; BIOINFORMATICS; DATA ANALYSIS; DNA SEQUENCE; ENERGY; PRIORITY JOURNAL; SENSITIVITY ANALYSIS;

EID: 78650926937     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2011.10508595     Document Type: Article

References (56)

1. Guo, F. B., and Lin, Y., 2009. J Biomol Struct Dyn, 26:413–420.
2. Cho, I. H., Lu, Z. R., Yu, J-R, Park, Y. D., Yang, J. M., Hahn, M. J., and Zou, F., 2009. J Biomol Struct Dyn, 27:331–345.
3. Sabbia, V., Romero, H., Musto, H., and Naya, H., 2009. J Biomol Struct Dyn, 27:361–369.
4. Zhao, J. N., Wang, Y., Zhao, B. S., and Chen, L. L., 2009. J Biomol Struct Dyn, 27:371–380.
5. Mukhopadhyay, P., and Ghosh, T. C., 2010. J Biomol Struct Dyn, 27:477–488.
6. Anbazhagan, P., Purushottam, M., Kumar, H. B. K., Mukherjee, O., Jain, S., and Sowdhamini, R., 2010. J Biomol Struct Dyn, 27:581–598.
7. Putta, P., and Mitra, C. K., 2010. J Biomol Struct Dyn, 27:599–610.
8. Liu, Z., Xu, Y., Wu, L., and Zhang, S., 2010. J Biomol Struct Dyn, 28:97–106.
9. Das, S., Mitra, S., and Chakrabarti, J., 2010. J Biomol Struct Dyn, 28:239–246.
10. Lu, Z. R., Seo, E., Yan, L., Yin, S. J., Si, Y. X., Qian, G. Y., Park, Y. D., and Yang, J. M., 2010. J Biomol Struct Dyn, 28:259–276.
11. Gojobori, T., 2009. J Biomol Struct Dyn, 26:840–841.
12. Atkinson, G., and Baldauf, S., 2009. J Biomol Struct Dyn, 26:841–842.
13. Aravind, L., 2009. J Biomol Struct Dyn, 26:843–843.
14. Huang, W., Guo, Y., and Zhang, J., 2009. J Biomol Struct Dyn, 26:599–608.
15. Jia, C., Liu, T., Zhang, X., Fu, H., and Yang, Q., 2009. J Biomol Struct Dyn, 26:763–769.
16. Zhang, S., and Wang, T., 2010. J Biomol Struct Dyn, 28:247–258.
17. Davison, D., 1984. Bull Math Biol, 46:437–474.
18. Waterman, M. S., 1989. Mathematical Methods for DNA Sequences Edited by:Waterman, M. S., 53–90. Boca Raton, Florida:CRC Press. Sequence alignments
19. Burge, C., Campbell, A. M., and Karlin, S., 1992. Proc Natl Acad Sci, 89:1358–1362.
20. Karlin, S., and Ladunga, I., 1994. Proc Natl Acad Sci, 91:12832–12836.
21. Bielinska-Waz, D., Waz, P., and Clark, T., 2007. Chem Phys Lett, 445:68–73.
22. Liao, B., and Ding, K., 2005. J Comput Chem, 26:1519–1523.
23. Zhang, Y. S., 2008. MATCH Commun Math Comput Chem, 60:313–324.
24. Chen, W., and Zhang, Y., 2009. MATCH Commun Math Comput Chem, 61:533–540.
25. Chen, W., and Zhang, Y., 2009. MATCH Commun Math Comput Chem, 61:781–788.
26. Vinga, S., and Almeida, J., 2003. Bioinformatics, 19:513–523.
27. Blaisdell, B. E., 1986. Proc Natl Acad Sci, 83:5155–5159.
28. Blaisdell, B. E., 1989. J of Mol Evol, 29:526–537.
29. Wu, T. J., Burke, J. P., and Davison, D. B., 1997. Biometrics, 53:1431–1439.
30. Wu, T. J., Hsieh, Y. C., and Li, L. A., 2001. Biometrics, 57:441–448.
31. Stuart, G. W., Moffett, K., and Baker, S., 2002. Bioinformatics, 18:100–108.
32. Li, M., Badger, J. H., Chen, X., Kwong, S., Kearney, P., and Zhang, H., 2001. Bioinformatics, 17:149–154.
33. Otu, H. H., and Sayood, K., 2003. Bioinformatics, 19:2122–2130.
34. Almeida, J. S., Carrico, J. A., Maretzek, A., Noble, P. A., and Fletcher, M., 2001. Bioinformatics, 17:429–437.
35. Pham, T. D., and Zuegg, J., 2004. Chem Phys Lett, 20:3455–3461.
36. Kantorovitz, M. R., Robinson, G. E., and Sinha, S., 2007. Bioinformatics, 23:1249–1255.
37. Dai, Q., Yang, Y., and Wang, T., 2008. Bioinformatics, 24:2296–2302.
38. Wu, T. J., Hsieh, Y. C., and Li, L. A., 2005. Bioinformatics, 21:4125–4132.
39. Panjkovich, A., and Melo, F., 2005. Bioinformatics, 21:711–722.
40. Breslauer, K. J., Frank, R., Blocker, H., and Marky, L. A., 1986. Proc Natl Acad Sci USA, 83:3746–3750.
41. Gotoh, O., and Tagashira, Y., 1981. Biopolymers, 20:1033–1042.
42. Vologodskii, A. V., Amirikyan, B. R., Lyubchenko, Y. L., and Frank-Kamenetskii, M. D., 1984. J Biomol Struct Dyn, 2:131–148.
43. Delcourt, S. G., and Blake, R. D., 1991. J Biol Chem, 266:15160–15169.
44. Doktycz, M. J., Golstein, R. F., Paner, T. M., Gallo, F. J., and Benight, A. S., 1992. Biopolymers, 32:849–864.
45. Record, M. T., Jr and Lohman, T. M., 1978. Biopolymers, 17:159–166.
46. Allawi, H. T., and SantaLucia, J., Jr. 1997. Biochemistry, 36:10581–10594.
47. SantaLucia, J., Jr., Allawi, H., and Seneviratne, P. A., 1996. Biochemistry, 35:3555–3562.
48. Sugimoto, N., Bajabo, S., Yoneyama, M., and Honda, K., 1996. Nucleic Acids Res, 24:4501–4505.
49. Crothers, D. M., and Zimm, B. H., 1964. J Mol Biol, 9:1–9.
50. DeVoe, H., and Tinoco, I., Jr. 1962. J Mol Biol, 4:500–517.
51. Gray, D. M., and Tinoco, I., Jr. 1970. Biopolymers, 9:233–244.
52. Borer, P. N., Dengler, B., Tinoco, I., Jr. and Uhlenkbeck, O. C., 1974. J Mol Biol, 86:843–853.
53. Uhlenbeck, O. C., Borer, P. N., Dengler, B., and Tinoco, I., Jr. 1973. J Mol Biol, 73:483–496.
54. SantaLucia, J., Jr. 1998. Proc Natl Acad Sci, 95:1460–1465.
55. Hide, W. A., Chan, L., and Li, W. H., 1992. J Lipid Res, 33:167–178.
56. Hide, W., Burke, J., and Davison, D., 1994. J Comput Biol, 1:199–215.