Secondary structure prediction Nucleic acid secondary structure

most methods nucleic acid secondary structure prediction rely on nearest neighbor thermodynamic model. common method determine probable structures given sequence of nucleotides makes use of dynamic programming algorithm seeks find structures low free energy. dynamic programming algorithms forbid pseudoknots, or other cases in base pairs not nested, considering these structures becomes computationally expensive small nucleic acid molecules. other methods, such stochastic context-free grammars can used predict nucleic acid secondary structure.

for many rna molecules, secondary structure highly important correct function of rna — more actual sequence. fact aids in analysis of non-coding rna termed rna genes . 1 application of bioinformatics uses predicted rna secondary structures in searching genome noncoding functional forms of rna. example, micrornas have canonical long stem-loop structures interrupted small internal loops.

rna secondary structure applies in rna splicing in species. in humans , other tetrapods, has been shown without u2af2 protein, splicing process inhibited. however, in zebrafish , other teleosts rna splicing process can still occur on genes in absence of u2af2. may because 10% of genes in zebrafish have alternating tg , ac base pairs @ 3 splice site (3 ss) , 5 splice site (5 ss) respectively on each intron, alters secondary structure of rna. suggests secondary structure of rna can influence splicing, potentially without use of proteins u2af2 have been thought required splicing occur.