ConStruct: A tool for thermodynamic controlled prediction of conserved secondary structure

Nucleic Acids Research

Volumn 27, Issue 21, 1999, Pages 4208-4217

  Lück, Rupert ^a   Gräf, Stefan ^a   Steger, Gerhard ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA PRECURSOR;

ALGORITHM; ARTICLE; GENETIC CONSERVATION; GENETIC PROCEDURES; PRIORITY JOURNAL; PROBABILITY; PROTEIN SECONDARY STRUCTURE; RNA STRUCTURE; THERMODYNAMICS;

ALGORITHMS; ANIMALS; BASE PAIR MISMATCH; BASE PAIRING; BASE SEQUENCE; CONSENSUS SEQUENCE; CONSERVED SEQUENCE; DATABASES, FACTUAL; HUMANS; MUTATION; NUCLEIC ACID CONFORMATION; RNA; RNA, SMALL NUCLEAR; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE; THERMODYNAMICS; USER-COMPUTER INTERFACE;

EID: 0033230822     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/27.21.4208     Document Type: Article

References (63)

1. Waterman, M.S. (1995) Introduction to Computational Biology, Maps, Sequences and Genomes. Chapman & Hall, London, UK.
2. Turner, D.H. and Sugimoto, N. (1988) Annu. Rev. Biophys. Biophys. Chem., 17, 167-192.
3. Wyatt, J.R., Puglisi, J.D. and Tinoco, I.,Jr (1989) Bioessays, 11, 100-106.
4. Westhof, E. and Michel, F. (1994) In Nagai, K. and Mattaj, I.W. (eds), RNA-Protein Interactions. IRL Press, Oxford, UK, pp. 25-51.
5. Schuster, P., Stadler, P.F. and Renner, A. (1997) Curr. Opin. Struct. Biol., 7, 229-235.
6. Conn, G.L. and Draper, D.E. (1998) Curr. Opin. Struct. Biol., 8, 278-285.
7. Beekwilder, M.J., Nieuwenhuizen, R. and van Duin, J. (1995) J. Mol. Biol., 247, 903-917.
8. Nussinov, R., Pieczenik, G., Griggs, J.R. and Kleitman, D.J. (1978) SIAM J. Appl. Math., 35, 68-82.
9. Waterman, M.S. and Smith, T.F. (1978) Math. Biosci., 42, 257-266.
10. Zuker, M. and Stiegler, P. (1981) Nucleic Acids Res., 9, 133-148.
11. Steger, G., Hofmann, H., Förtsch, J., Gross, H.J., Randles, J.W., Sänger, H.L. and Riesner, D. (1984) J. Biomol. Struct. Dyn., 2, 543-571.
12. Jaeger, J.A., Turner, D.H. and Zuker, M. (1990) Methods Enzymol., 183, 281-306.
13. McCaskill, J.S.M. (1990) Biopolymers, 29, 1105-1119.
14. Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H. (1999) J. Mol. Biol., 288, 911-940. http://www.ibc.wustl.edu/~zuker/mfold-3.0.html
15. Zuker, M., Mathews, D.H. and Turner, D.H. (1999) In Barciszewski, J. and Clark, B.F.C. (eds), RNA Biochemistry and Biotechnology. NATO ASI Series, Kluwer, Academic Publishers, Dordrecht, The Netherlands. http://www.ibc.wustl.edu/~zuker/seqanal
16. Le, S.Y. and Zuker, M. (1991) J. Biomol. Struct. Dyn., 8, 1027-1044.
17. Le, S.Y., Zhang, K. and Maizel, J.V.,Jr (1995) Comput. Biomed. Res., 28, 53-66.
18. Davis, J.P., Janjic̀, N., Pribnow, D. and Zichi, D.A. (1995) Nucleic Acids Res., 23, 4471-4479.
19. Lück, R., Steger, G. and Riesner, D. (1996) J. Mol. Biol., 258, 813-826.
20. Hofacker, I.L., Fekete, M., Flamm, C., Huynen, M.A., Rauscher, S., Stolorz, P.E. and Stadler, P.F. (1998) Nucleic Acids Res., 26, 3825-3836.
21. Antao, V.P., Lai, S.Y. and Tinoco, I.,Jr (1991) Nucleic Acids Res., 19, 5901-5905.
22. Antao, V.P. and Tinoco, I.,Jr (1992) Nucleic Acids Res., 20, 819-824.
23. Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, S., Tacker, M. and Schuster, P. (1994) Monatsh. Chem., 125, 167-188.
24. Hofacker, I. (1998) http://www.tbi.univie.ac.at/~ivo/RNA/
25. Tinoco, I.,Jr, Uhlenbeck, O.C. and Levine, M.D. (1971) Nature, 230, 362-367.
26. Gilbert, D.G. (1993) ftp://ftp.bio.indiana.edu/molbio/readseq/
27. Schneider, T.D., Stormo, G.D., Gold, L. and Ehrenfeucht, A. (1986) J. Mol. Biol., 188, 415-431.
28. Gutell, R.R., Power, A., Hertz, G.Z., Putz, E.J. and Stormo, G.D. (1992) Nucleic Acids Res., 20, 5785-5795.
29. Eddy, S.R. and Durbin, R. (1994) Nucleic Acids Res., 22, 2079-2088.
30. Gautheret, D., Damberger, S.H. and Gutell, R.R. (1995) J. Mol. Biol., 248, 27-43.
31. Chiu, D.K. and Kolodziejczak, T. (1991) Comp. Appl. Biosci., 7, 347-352.
32. Scriptics (1999) http://www.scriptics.com/
33. Nijtmans, J. (1998) http://home.wxs.nl/~nijtmans/
34. Phillips, S.C., Watkins, N.J. and Turner, P.C. (1996) EMBL ID XBU715KB, GenBank accession no. Z543132E
35. Phillips, S.C. and Birnstiel, M.L. (1992) EMBL ID XLU7SNRG, GenBank accession no. X64404.
36. Matthews, P. (1996) EMBL ID HSL191F1, GenBank accession no. Z68756.
37. Mowry, K.L. and Steitz, J.A. (1987) Science, 238, 1682-1687. EMBL ID HSSRU7RP, GenBank accession no. M17910.
38. Cotten, M., Gick, O., Vasserot, A., Schaffner, G. and Birnstiel, M.L. (1988) EMBO J., 7, 801-808. EMBL ID MMU7SNR, GenBank accession no. X07183.
39. Gruber, A., Soldati, D., Burri, M. and Schümperli, D. (1991) Biochim. Biophys. Acta, 1088, 151-154. EMBL ID MMU7, GenBank accession no. X54748.
40. De Lorenzi, M., Rohrer, U. and Birnstiel, M.L. (1986) Proc. Natl Acad. Sci. USA, 83, 3243-3247. EMBL ID PMUG7A1-PMUG7A5, GenBank accession nos M13307-M13311.
41. Schmitz, M. and Steger, G. (1992) Comp. Appl. Biosci., 8, 389-399.
42. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) Nucleic Acids Res., 22, 4673-4680.
43. Jeanmougin, F., Thompson, J.D., Gouy, M., Higgins, D.G. and Gibson, T.J. (1998) Trends Biol. Sci., 23, 403-405.
44. Thompson, J. and Jeanmougin, F. (1998) ftp://ftp.ebi.ac.uk/pub/software/ unix/clustalw/
45. Genetics Computer Group (1999) Wisconsin Package. Genetics Computer Group, Madison, WI. http://www.gcg.com/
46. Bruccoleri, R.E. and Heinrich, G. (1988) Comp. Appl. Biosci., 4, 167-173. ftp://snark.wustl.edu/pub/naview.tar.Z
47. De Rijk, P. and De Wachter, R. (1997) Nucleic Acids Res., 25, 4679-4684. http://rrna.uia.ac.be/rnaviz/
48. Weiser, B. and Noller, H.F. (1999) ftp://fangio.ucsc.edu/pub/XRNA
49. Birnstiel, M.F.L. and Schaufele, F.J. (1988) In Birnstiel, M.L. (ed.), Structure and Function of Major and Minor Small Nuclear Ribonucleoprotein Particles. Springer Verlag, Heidelberg, Germany, pp. 155-182.
50. Mowry, K.L. and Steitz, J.A. (1988) Trends Biol. Sci., 13, 447-451.
51. Stösser, G., Tuli, M.A., Lopez, R. and Sterk, P. (1999) Nucleic Acids Res., 27, 18-24. http://www.ebi.ac.uk/embl/
52. Zwieb, C. (1998) http://psyche.uthct.edu/dbs/uRNADB/uRNADB.html
53. Zuker, M. and Jacobson, A.B. (1998) RNA, 4, 669-679.
54. Smith, G.J., Donello, J.E., Lück, R., Steger, G. and Hope, T.J. (1998) Nucleic Acids Res., 26, 4818-4827.
55. Matoušek, J., Junker, V., Vrba, L., Schubert, J., Patzak, J. and Steger, G. (1999) Gene, in press.
56. Larsen, N. and Zwieb, C. (1991) Nucleic Acids Res., 19, 209-215.
57. Gaspin, C. and Westhof, E. (1995) J. Mol. Biol., 254, 163-174.
58. Chetouani, F., Monestié, P., Thébault, P., Gaspin, C. and Michot, B. (1997) Nucleic Acids Res., 25, 3514-3522.
59. Tabaska, J.E., Cary, R.B., Gabow, H.N. and Stormo, G.D. (1998) Bioinformatics, 14, 691-699.
60. Rivas, E. and Eddy, S.R. (1999) J. Mol. Biol., 285, 2053-2068.
61. Abrahams, J.P., van den Berg, M., van Batenburg, E. and Pleij, C. (1990) Nucleic Acids Res., 18, 3035-3044.
62. van Batenburg, F.H., Gultyaev, A.P. and Pleij, C.W. (1995) J. Theor. Biol., 174, 269-280.
63. Gultyaev, A.P., van Batenburg, F.H. and Pleij, C.W. (1999) RNA, 5, 609-617.