I have group I intron sequences (full length, DNA) of chlorophycean microalgae. I want to create secondary structure of the gene. Which is the beat tool/software for creating secondary structures? should I translate the sequences to RNA before secondary structure construction?
Good morning Preetha!
Here's an article that can help with your questions.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6306197/pdf/pone.0208929.pdf
Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure
David H. Mathews, Jeffrey Sabina, Michael Zuker and Douglas H. Turner J. Mol. Biol. (1999) 288
The secondary structure of the unusually long 18S ribosomal RNA of the myxozoan Sphaerospora truttae and structural
evolutionary trends in the Myxozoa
Astrid S. Holzer , Rod Wootten, Christina Sommerville
Give more detailed idea on secondary structures of RNA
You may find these resources useful:
- The Group I Intron Sequence and Structure Database (GISSD): http://www.rna.whu.edu.cn/gissd/
- RNAstructure: a complete package for RNA and DNA secondary structure prediction and analysis. rna.urmc.rochester.edu/RNAstructure.html
- ProbKnot software for predicting RNA secondary structure including pseudoknots: Article ProbKnot: Fast prediction of RNA secondary structure includi...
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