An improved random-walk approach for visualizing periodicities hidden in biological sequences

Abstract

Presently, substantial studies have been conducted to investigate periodicities hidden in biological sequences. Among them, the Self-Adaptive Spectral Rotation (SASR) method is said to be an efficient tool to visualize the 3-bp periodicity (TP) in DNA sequences. It outputs a random walk, i.e., TP walk, in the complex plane for any query sequence. And the TP-intensive regions in the sequence can be visually discriminated from the non-TP ones in the walk. In this paper, the behaviors of the walks for non-TP sequences are further investigated qualitatively. A slightly leftward trend (an abnormity) in such walks is observed, which is not reported in the previous SASR literatures. An improved SASR, named the mature SASR, is proposed, in order to eliminate the abnormity, correct the TP walks, and provide a better visualization.