Hi! I'm using an R program and I have a large table where I have UTR sequences.
I would like to parse these sequences from within R (or python) for secondary structure prediction and finding sequential and structural motifs.
I've been playing with it for a long time and in all libraries: ViennaRNA, RRNA or RNAstructure but I can't use them from the R level because various messages pop up.
And a question, do you know any libraries for RNA analysis. Forgive me for asking you such a question, but I'm a biotechnologist trying bioinformatics.
Martyna Kordyś There are various R and Python tools available for RNA secondary structure prediction and motif analysis. Here are several possibilities:
1. RNAstructureR: This package interfaces with the RNAstructure program, which predicts RNA secondary structure and folding free energy. It also contains RNA motif analysis functions.
2. RNAStructure is a wrapper for the RNAstructure program that allows you to utilize RNAstructure functions from within R.
3. RnaSeqMap: This package contains utilities for evaluating RNA structure and motifs using data from RNA sequencing.
Python packages include:
1. ViennaRNA: This package predicts RNA secondary structure, folding free energy, and RNA-RNA interactions.
2. Biopython is a Python library that offers methods for altering and analyzing biological data, such as RNA sequencing and structure analysis.
This package contains RNAstructure.
It's difficult to comment on the error messages you're seeing when attempting to utilize these packages without further information. But, I recommend looking through the package documentation and forums to see if anybody else has had similar problems and how they were addressed. You might also try contacting the package maintainers for assistance.
I hope this helps, and best wishes with your bioinformatics work!
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