RNA-structure and Prediction

RNA Structure and Prediction

Like protein, RNA also has secondary structure, tertiary structure, and quaternary stricture, too.	© wiki]

In Secondary Structure, it could form:

• Double helix
• Stem-loop structure
• Pseudoknots

wikipedia listed a bunch of tools for RNA secondary structure prediction.

Online structure prediction servers:

• Mathews Lab
• RNAfold

RAN Secondary Structure Format.

• DB format (Dot bracket)
  • Unpaired nucleotides are indicated with the . or : characters.
  • Matching pairs of parentheses indicate base pairs.
  • To indicate non-nested base pairs (pseudoknots), additional brackets may be used: [], {}, or <>.
    Example:

GGUGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGCAUGUAGUACC
((((((((((((((.[[[[[[..))))).....]]]]]]........)))))...))))

Secondary Structure Predict

Seq:

UGAGUGGUGUUGUUGGCUGCAUUAUGAUGUUGGUUAUAUUCUGGUUUUCUUCCACUCAACAACAACAACAACACGCAGUAGUAGAAGCAACAACAAGCAUAUAACCAACAUCAUAAUGCAGCCAACAACACCACUCA

Website: RANfold
Result:

RNA Secondary Structure Plot

RNAplot from ViennaRNA

RNAplot tmp.db # RNAfold results

RRNA in R

install.package("RRNA")
library(RRNA)
coord=ct2coord(ct)
ct=makeCt( "(((((((((((((((((((((((((((((((((((((((.((.(((((((((.(((..((.................))))).)))).)).))).)).)))))))))))))))))))))))))))))))))))))))", "UGAGUGGUGUUGUUGGCUGCAUUAUGAUGUUGGUUAUAUUCUGGUUUUCUUCCACUCAACAACAACAACAACACGCAGUAGUAGAAGCAACAACAAGCAUAUAACCAACAUCAUAAUGCAGCCAACAACACCACUCA")
RNAPlot(coord,hl=c("GGGUUU","AAAUUU"),seqcols=c(2,4),labTF=F)

Python

pip install RNA forgi