Löwes, Benedikt: Methods for the identification of common RNA motifs. 2017
Inhalt
- Contents
- 1 Motivation & outline
- 2 Background
- 2.1 General definitions
- 2.2 (Context-free) grammars and languages
- 2.3 The RNA molecule
- 2.3.1 Structural levels
- 2.3.2 Prediction of secondary structures
- 2.3.3 Identifying potentially functional RNAs
- 2.4 Index data structures
- 3 Exact Matching of RNA secondary structures of viral genomes
- 3.1 Types of convergence
- 3.2 Preparation of the viral data set
- 3.3 Strategy for exact matching
- 3.3.1 Folding genome sequences using windows
- 3.3.2 Exact matching using maximal repeats and suffix arrays
- 3.4 Known families in clusters
- 3.5 Filtering of the clusters
- 3.6 Summary & additional steps
- 4 The viable suffix tree
- 4.1 Previous work on constrained suffix trees
- 4.2 Pruning the suffix tree
- 4.3 Definition
- 4.4 Direct construction of viable suffix trees
- 4.5 Computation of lvp lengths for RNAs
- 4.6 Finding maximal repeated pairs in viable suffix trees
- 4.7 Implementation & benchmarks
- 4.8 Conclusion
- 5 An unbiased RNA benchmark data set
- 5.1 Benchmark data sets for biological data
- 5.2 The BRaliBase dent
- 5.3 Explaining the BRaliBase dent
- 5.4 Concluding the dent
- 6 Seed based detection of common RNA motifs
- 6.1 Sequence and structure matches using seed and extend
- 6.2 Identifying RNA motifs using sequence and structure seeds
- 6.2.1 Seeds and their hash values
- 6.2.2 Creating database from hash values for seeds
- 6.2.3 Filter windows for duplicates and by complexity
- 6.2.4 Identification of common motifs in windows
- 6.2.5 Combining the common seeds among all windows
- 6.2.6 Summary: combining all steps
- 6.3 Application of the algorithm
- 6.3.1 Seed sequences of the hammerhead ribozyme families
- 6.3.2 Taxonomically distant sequences of the hammerhead family
- 6.4 Discussion
- 7 Conclusion
- Appendices
- A Complete pruning of the suffix tree
- B Details about BRaliBase benchmarks
- B.1 Details about programs used for benchmark re-computation
- B.2 RNAforecast: a Plan C approach
- B.3 Comparison of RNA-unchained modes
- B.4 Detailed plots for all RNA families individually
- Bibliography