RNA-SSPT: RNA Secondary Structure Prediction Tools
- Resource Type
- Authors
- Muhammad Afzal; Tanzeela Hanif; Freed Ahmad; Hifza Ahmad; Shahid Mahboob; Tahsin Gulzar; Salah U. Din
- Source
- Bioinformation
- Subject
- dot net
Computer science
Base pair
Sequence analysis
In silico
RNA
General Medicine
computer.software_genre
C#
Visualization
Nucleic acid secondary structure
RNA secondary structure prediction
Nussinov algorithm
Data mining
Nucleic acid structure
computer
Algorithm
Protein secondary structure
Software
- Language
- ISSN
- 0973-2063
The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes.