PLANAR: RNA Sequence Alignment using Non-Affine Gap Penalty and Secondary Structure

An important component of bioinformatics research is aimed at finding evolutionary relationships among species, since it allows us to better understand various important biological functions as they emerged in these species. These tools simultaneously trace the associated evolutionary history. In this context, sequence alignment is commonly used to understand similarities among the species by comparing their genomic, transcriptomic and proteomic sequence data. In our earlier research, we devised PLAINS (PiecewiseLinear Alignment with Important Nucleotide Seeker) to align genomic DNA sequences using a general class of gap distribution model. This paper proposes PLANAR (Piecewise-Linear Alignment for Nucleotides Arranged as RNA), a variant of PLAINS designed for aligning RNA sequences, while properly accounting for their secondary structures. This paper presents an overview of the PLANAR algorithm, and compares it to other competing RNA alignment tools, while emphasizing many interesting correlations discovered in the process.