Finding specific RNA sequence motifs using digital filters

Local distinct structural elements, called motifs, in RNA sequences are strictly correlated with their function. Due to the enormous increase of genomic data in recent times, highly effective computational algorithms are in greater demand for identification of such motifs in RNA sequences. In this work, a digital signal processing approach using statistically optimal null filter (SONF) is developed for finding specific motifs in an RNA sequence. The instantaneous matched filter in SONF determines the degree of local alignment between the motif and the windowed RNA sequence being compared. Through example the effectiveness of the proposed approach is illustrated. In particular, the proposed method is highly efficient in identifying similar motifs in large RNA sequences.