A procedure for RNA pseudoknot prediction

• Published in: Bioinformatics Vol. 8; no. 3; pp. 243 - 248
• Main Authors: Chen, Jih-H., Le, Shu-Yun, Maizel, Jacob V.
• Format: Journal Article Web Resource
• Language: English
• Published: Washington, DC Oxford University Press 01.06.1992; Oxford
• Subjects: Algorithms; Analytical, structural and metabolic biochemistry; Base Sequence; Biological and medical sciences; Fundamental and applied biological sciences. Psychology; Infectious bronchitis virus - chemistry; Infectious bronchitis virus - genetics; Molecular Sequence Data; Nucleic Acid Conformation; Nucleic acids; Original Papers; RNA - chemistry; RNA - genetics; Rna, ribonucleoproteins; RNA, Viral - chemistry; RNA, Viral - genetics; Software; Tobacco Mosaic Virus - chemistry; Tobacco Mosaic Virus - genetics; Computer program; RNA; Molecular structure; Computerized processing; Prediction; FORTRAN; Software; Method; Secondary structure; Algorithm
• ISSN: 1367-4803; 0266-7061; 1460-2059
• DOI: 10.1093/bioinformatics/8.3.243

The RNA pseudoknot has been proposed as a significant structural motif in a wide range of biological processes of RNAs. A pseudoknot involves intramolecular pairing of bases in a hairpin loop with bases outside the stem of the loop to form a second stem and loop region. In this study, we propose a method for searching and predicting pseudoknots that are likely to have functional meaning. In our procedure, the orthodox hairpin structure involved in the pseudoknot is required to be both statistically significant and relatively stable to the others in the sequence. The bases outside the stem of the hairpin loop in the predicted pseudoknot are not entangled with any formation of a highly stable secondary structure in the sequence. Also, the predicted pseudoknot is significantly more stable than those that can be formed from a large set of scrambled sequences under the assumption that the energy contribution from a pseudoknot is proportional to the size of second loop region and planar energy contribution from second stem region. A number of functional pseudoknots that have been reported before can be identified and predicted from their sequences by our method.