Pattern discovery in RNA secondary structure using affix trees

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 2676, Issue , 2003, Pages 278-294

  Mauri, Giancarlo ^a   Pavesi, Giulio ^a  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; FORESTRY; PATTERN MATCHING; RNA; TREES (MATHEMATICS);

BI-DIRECTIONAL SEARCH; INDEXING STRUCTURES; PATTERN DISCOVERY; PREDICTION METHODS; RNA SECONDARY STRUCTURES; SECONDARY STRUCTURES; SEQUENCE INFORMATIONS; STRUCTURAL INFORMATION;

ALGORITHMS;

EID: 1242296643     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-44888-8_21     Document Type: Article

References (23)

1. Gesteland, R., Cech, T., Atkins, J., (eds.): The RNA World. Cold Spring Harbor Laboratory Press, New York (1999)
2. Simons, R., Grumberg-Magnago, M., (eds.): RNA Structure and Function. Cold Spring Harbor Laboratory Press, New York (1998)
3. Fox, G., Woese, C.: 5s rna secondary structure. Nature 256 (1975) 505-507
4. Westhof, E., Auffinger, E., Gaspin, C.: Dna and rna structure prediction. In: DNA - Protein Sequence Analysis, Oxford (1996) 255-278
5. Stephan, W., Parsch, J., Braverman, J.: Comparative sequence analysis and patterns of covariation in rna secondary structures. Genetics 154 (2000) 909-921
6. Gorodkin, J., Heyer, L., Stormo, G.: Finding common sequence and structure motifs in a set of rna sequences. Nucleic Acids Research 25 (1997) 3724-3732
7. Gorodkin, J., Stricklin, S., Stormo, G.: Discovering common stem-loop motifs in unaligned rna sequences. Nucleic Acids Research 29 (2001) 2135-2144
8. Maass, M.: Linear bidirectional on-line construction of affix trees. Proc. of CPM 2000, Lecture Notes in Computer Science 1848 (2000) 320-334
9. Gusfield, D.: Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press, New York (1997)
10. Marsan, L., Sagot, M.: Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification. Journal of Computational Biology T (2000) 345-360
11. Sagot, M.: Spelling approximate repeated or common motifs using a suffix tree. Lecture Notes in Computer Science 1380 (1998) 111-127
12. Pavesi, G., Mauri, G., Pesole, G.: An algorithm for finding signals of unknown length in dna sequences. Proc. of ISMB '01, Bioinformatics 17 (2001) S207-S214
13. Hertz, G., Hartzell, G., Stormo, G.: Identification of consensus patterns in unaligned dna sequences known to be functionally related. Comput.Appl.Biosci. 6 (1990) 81-92
14. Hertz, G., Stormo, G.: Identifying dna and protein patterns with statistically significant alignment of multiple sequences. Bioinformatics 15 (1999) 563-577
15. Zucker, M., Matthews, D.H., Turner, D.H.: Algorithms and thermodynamics for rna secondary structure prediction: a practical guide. In: RNA Biochemistry and Biotechnology, NATO ASI Series, Kluwer Academic Publishers (1999) 11-43
16. Hofacker, I., Fontana, W., Stadler, P., Bonhoeffer, S., Tacker, M., Schuster, P.: Fast folding and comparison of rna secondary structures. Monatshefte f Chemie 125 (1994) 167-188
17. Wuchty, S., Fontana, W., Schuster, P.: Complete suboptimal folding of rna and the stability of secondary structures. Biopolymers 49 (1999) 145-165
18. Ward, J.: Hierarchical grouping to optimize an objective function. Journal of the American Statistical Association 58 (1963) 236-244
19. Hentze, M., Kuhn, L.: Molecular control of vertebrate iron metabolism: mrna based regulatory circuits operated by iron, nitric oxide and oxidative stress. Proc. Natl. Acad. Sci. USA 93 (1996) 8175-8182
20. Williams, A., Marzluff, W.: The sequence of the stem and flanking sequences at the 3′ end of histone mrna are critical determinants for the binding of the stem-loop binding protein. Nucleic Acids Research 23 (1996) 654-662
21. Walter, A., Turner, D., Kim, J., Lyttle, M., Muller, P., Mathews, D., Zuker, M.: Coaxial stacking of helices enhances binding of oligoribonucleotides. PNAS 91 (1994) 9218-9222
22. Mathews, D., Sabina, J., Zucker, M., Turner, D.: Expanded sequence dependence of thermodynamic parameters provides robust prediction of rna secondary structure. Journal of Molecular Biology 288 (1999) 911-940
23. Pain, V.: Initiation of protein synthesis in eukaryotic cells. Eur. J. Biochem. 236 (1996) 747-771