A structure based similarity measure for nucleic acid sequence comparison

Subscribe (Full Service)


	Search: The ACM Digital Library The Guide

	Feedback

A structure based similarity measure for nucleic acid sequence comparison

Full text

Pdf (861 KB)

Source

Annual Conference on Research in Computational Molecular Biology archive
Proceedings of the second annual international conference on Computational molecular biology table of contents

New York, New York, United States

Pages: 173 - 181

Year of Publication: 1998

ISBN:0-89791-976-9

Authors

Rongxiang Liu	Institute for Biomedical Computing, Washington University, St. Louis, Missouri
Tom W. Blackwell	Institute for Biomedical Computing, Washington University, St. Louis, Missouri
David U. States	Institute for Biomedical Computing, Washington University, St. Louis, Missouri

Sponsor

SIGACT: ACM Special Interest Group on Algorithms and Computation Theory

Publisher

ACM New York, NY, USA

Bibliometrics

Downloads (6 Weeks): 3, Downloads (12 Months): 19, Citation Count: 0

Additional Information:

references index terms collaborative colleagues

Tools and Actions:	Request Permissions Review this Article Save this Article to a Binder Display Formats: BibTeX EndNote ACM Ref

DOI Bookmark:	Use this link to bookmark this Article: http://doi.acm.org/10.1145/279069.279112 What is a DOI?

REFERENCES

Note: OCR errors may be found in this Reference List extracted from the full text article. ACM has opted to expose the complete List rather than only correct and linked references.

	1	AUemann, ILK. and Egli, M. (1997) DNA recognition and bending. Chemistry and Biology 4, 643-650.
	2	Altschul, S.F. (1991) Amino acid substitution matrix from an information theoretic perspective. J. Mol. Biol. 219, 555-565.
	3	Altschul, S.F.;Gish,W.~er, W.;Myers,E.W. and Lipman,DJ. (1990) Basic local alignment tool. J. Mol. Biol. 215, 403-410.
	4	Bansal, M., Bhattacharyya. D. and Ravi, B. (1995) NUP~ and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. CABIOS 11,281-287.
	5	Bansal, M (1996) Observed DNA crystal structure variations and its implication to DNA-protein interaction. Biomoleeular Structure and Dynamics. Proceedings of the 1995 conversation in discipline biomoleeular stereodunamics. 112-134.
	6	Benham,CJ. (1993) Sites of predicted stress-induced DNA dulpex destab'fiiz~fion occur preferentially at regulatory loci. PNAS. USA. 90, 2999-3003.
	7	Berman, H.M.; Olson,W.IC; Beveridge, D.L.; Westbrook, J.; Gelbin, A. (1992) The nucleic acid database. Biophys. J. 63, 751-759.
	8	Bhattacharyya, D. and Bansal,M (1990) Local variability and base sequence effects in DNA crystal structure. J. Biomol. Stmct. Dynam. 8, 539-572.
	9	Bolshoy, A.;McNamaraP.;Hmton,R.E. and Trifonov, E.N. (1991) Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. PNAS, USA. 88, 2312--2316.
	10	Brown,M.L.Schroth,G.P.;Gottesfeld,J.M. and Bazett- Jones,D.P. (1996) Protein and DNA require-ments for the transcription factor IIIA-induced distortion of the 5S rRNA gene promoter. J. Mol. Biol. 262, 600-614.
	11	Bucher, P. and Trifonov,E.N. (1986) Compilation and analysis of eukaryotic Pol II promoter sequences. Nucleic Acids Res. 14, 10009-10026.
	12	Cacchione,S. ;De Santi,P.; Foti, D.P.; Palleschi,A. and Savino, M.(1989) Periodical polydeoxynucleofides and DNA curvature. Biochemistry, 28, 8706-8713.
	13	Dickerson, RE. (1992) DNA structure from A to Z. Methods in Enzymology, vo1211, 67-110.
	14	Dickerson, R.E.(1983) Base sequence and helix structure variations in B and A-DNA. 3.MoI. Biol. I66, 419-441.
	15	Dickers~n'R'E';Drew'H'R';C~nner'B'N' ;Wing'R'M' ;Fr atini,A.V, and Kopka,M.L.(1982) The anatomy of A-, B-, and Z-DNA. Science, 216, 475-485.
	16	Dunham,S.U. and Lippard,SJ. (1997) DNA sequence context and protein composition modulate HMG- domain protein recognition of cisplatin-modified DNA. Biochemistry. 36, 11428-11436.
	17	Fitzgerald,D J.;Dryden,G.L.;Bronson,E.C.;Williams,J. S. and Anderson,J2q. (1994) Conserved patterns of bending in satellite and nucleosome positioning DNA. J. Mol. Biol. 269, 21303-21314.
	18	Goodsell,D.V. and Dickerson,R.E. (1994) Bending and curvature calculations in B-DNA. Nucleic Acids Res. 22,5497-5503.
	19	Gorin, A.A; Zhurkin, V.B. and Olson, W.K.(1995) B- DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247.34-48.
	20	Ghosh, D. (1992) TFD: the transcription factor database (TFD). Nucleic Acids Res. 20, 2091-2093.
	21	Grzeskowiak,~; Goodsell,D. S.; KaczorGrzeskowiak, M.;Cascio,D. and Dickerson,R_E. (1993) Crystallographic analysis of C-C-A-A-G-C-T-T-G-C and its implications for bending in B-DNA. Biochemistry,32, 8923- 8931.
	22	Hartmann,B.; Piazzola, D. and Lavery, R. (1993) BI- BH transitions in B-DNA. Nucleic Acids Research 21, 561-568.
	23	Ioshikhes,I.;B olshoy, A.;Derenshteyn,K.;B orodovsky, M.'Trifonov, E.N. (1996) Nueleosome DNA sequence pattern revealed by multiple alignment of experimental mapped sequences. J. Mol. Biol. 262,129-139.
	24	Kopka, M.L; GoodseU,D.S.; Baikalov,I.;Grzeskowiak, IC;Cascio,D. and Diekerson,R.E. (1994) Crystal structure of a covalent DNA-Drug adduet: Anthramyein bound to C-C-A-A-C-G-T-T-G-G and a molecular explanation of specificity. Biochemistry. 33,13593- 13610.
	25	Love,~J.;Li~;Case,D.A.;Giese,K.;Grosschedl,R. and Wright, RE. (1995) Structure basis for DNA bending by the architectural transcription factor LEF-1. Nature, 376, 791-795.
	26	Olson,W. IC and Zhang, P. (1991) Computer simulation of DNA supercoiling. Method in Enzymology, 203, 4O3-432.
	27	Otwinowsld,Z.;Zhang,tLG.;Lawson,C.L.;Sigler,P.B. (1988) Crystal s tmeture of trp repressorloperator complex at atomic resolution. Nature, 335, 321-329.
	28	Person, W.tL;and Lipman,DJ. (1988) Improved tools for biological sequence comparison. ?NAS. USA. 85, 2444-2448.
	29	Schlick, T and Olson, W. IC(1992) Supercoiled DNA energetics and dynamics by computer simulation. J. Mol. Biol. 223. 1089-1119.
	30	Schumacher, M.A.; Glasfeld, A.;Zalkin,H. and Brennan, R.G. (1997) The X-ray structure of the purR-gurinepuff operator eomplex reveals the contributions of complementary electrostatics surfaces and a water mediated hydrogen bond to co-repressor specificity and binding affinity. J. Biol. Chem. 272, 22648-22653.
	31	Shakked,Z.; GuzikevichGuerstein,G.;Frol ow, F.;Rabino vich,D, and Sigler, P.B. (1994) Determine ofrepressor/ operator recognition from the structure of the trp operator binding site. Nature. 368, 469-473.
	32	Sivolob, AN. and Khrapunov, S.N.(1995) Translational positioning of nucleosomes on DNA: The role of sequence-dependent istropic DNA bending stiffness. J. Mol.Biol. 247, 918-931.
	33	Sjottem, E.; Anderson, C.and Johanson, T. (1997) Structural and functional analysis of DNA bending induced by Spl family transcription factor. J. Mol. Biol. 267,490-504.
	34	Sun,D. and Hurley, L.H. (1994) Cooperative bending of the 21-base-pair repeats of the SV40 viral early promoter by human Spl. Biochemistry. 33, 9578-9587.
	35	Tung,C.S. and Harvey,S.C. (1986a) Computer graphics program to reveal the dependence of the gross three-dimensional structure of the B-DNA doublehelix on primary structure. Nucleic Acid Res. 14, 381- 387.
	36	Tung, C.S. and Harvey,S.C. (1986b) Base sequence, local helix structure, and macroscopic curvature of A- DNA and B-DNA. J. Mol. Biol. 261,3700-3709.
	37	West, A.G.; Shore, P. and Sharrocks, A.D. (1997) DNA binding by MADS-box transcription factors: a molecular mechanism for differential DNA bending. Mol. Cell. Biol. 17, 2876-2887.
	38	Yanagi, IC; Prive, G.G. and Dickerson, R .E. (1991) Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. J. Mol. Biol. 217,201- 214.