Secondary structure prediction for aligned RNA sequences

Journal of Molecular Biology

Volumn 319, Issue 5, 2002, Pages 1059-1066

  Hofacker, Ivo L ^a   Fekete, Martin ^a   Stadler, Peter F ^a,b  

^a UNIVERSITY OF VIENNA   (Austria)

^b SANTA FE INSTITUTE   (United States)

Author keywords

Compensatory mutations; Conserved substructures; RNA secondary structure prediction

Indexed keywords

MESSENGER RNA;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; ESCHERICHIA COLI; MOLECULE; NONHUMAN; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RELIABILITY; RNA SEQUENCE; SEQUENCE ALIGNMENT; THERMODYNAMICS; THERMOSTABILITY;

EID: 0036301332     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00308-X     Document Type: Article

References (35)

1. Compilation of tRNA sequences and sequences of tRNA genes
2. A story: Unpaired adenosine bases in ribosomal RNA
3. The RDP-II (ribosomal database project)
4. The European small subunit ribosomal RNA database
5. 5 S ribosomal RNA database Y2K
6. The European large subunit ribosomal RNA database
7. The ribonuclease P database
8. SRPDB (signal recognition particle database)
9. The tmRNA website: Invasion by an intron
10. Simultaneous solution of the RNA folding, alignment, and proto-sequence problems
11. Automated alignment of RNA sequences to pseudo-knotted structures
12. Finding common sequences and structure motifs in a set of RNA molecules
13. Finding the most significant common sequence and structure motifs in a set of RNA sequences
14. Predicting common foldings of homologous RNAs
15. Thermodynamic prediction of conserved secondary structure: Application to the RRE element of HIV, the tRNA-like element of CMV, and the mRNA of prion protein
16. ConStruct: A tool for thermodynamic controlled prediction of conserved secondary structure
17. Automatic detection of conserved RNA structure elements in complete RNA virus genomes
18. Automatic detection of conserved base-pairing patterns in RNA virus genomes
19. RNA secondary structure prediction based on free energy and phylogenetic analysis
20. Prediction of common folding structures of homologous RNAs
21. Algorithms for loop matching
22. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure
23. Optimal computer folding of larger RNA sequences using thermodynamics and auxiliary information
24. The equilibrium partition function and base-pair binding probabilities for RNA secondary structure
25. Inferring consensus structure from nucleic acid sequences
26. Higher order structural elements in ribosomal RNAs: Pseudoknots and the use of noncanonical pairs
27. Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods
28. On finding all suboptimal foldings of an RNA molecule
29. Complete suboptimal folding of RNA and the stability of secondary structures
30. Using multiple alignments and phylogenetic trees to detect RNA secondary structure
31. Translational and structural requirements of the early nodulin gene enod40, a short-open reading frame-containing RNA, for elicitation of a cell-specific growth response in the alfalfa root cortex
32. RNA localization: Different zipcodes, same postman?
33. Non-coding, mRNA-like RNAs database Y2K
34. CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties, and weight matrix choice
35. Energy directed folding of RNA sequences