DrovePred: Server for DNA stem and BIME's prediction using Particle Swarm Optimization

Abstract

Stem prediction has been a problem that has attracted the attention of bioinformaticians for a long time. With important role in central dogma of prokarryotes and eukaryotes alike along with known role in viral genome encapsidation, the importance of DNA/RNA stems cannot be neglected. Bacterial interspersed Mosaic Elements known as BIMEs play an important regulatory role in bacterial replication. Similarly, predicted DNA thermodynamic properties can help us in manipulating and understanding the dynamics of DNA denaturation and renaturation in a far better manner. Particle Swarm Optimization (PSO) is an important evolutionary algorithm based on swarm intelligence to solve NP optimization problems. This paper proposes a PSO based algorithm for predicting DNA/RNA stems, BIMEs and DNA thermodynamic properties.