Challenges in the analysis of viral metagenomes

Rose, Rebecca; Constantinides, Bede; Tapinos, Avraam; Robertson, David L; Prosperi, Mattia

We recently proposed a method based on numerical sequence representations and digital signal processing data transformation (SPDT) approaches to reduce the size of working datasets, permitting fast and sensitive read alignment and de novo assembly of diverse viral populations (Tapinos et al. 2015) . SPDT methods, such as the discrete Fourier transform (DFT) (Agrawal, Faloutsos, and Swami 1993) , and discrete wavelet transform (DWT) (Percival and Walden 2006) (Fig. 2) , are used to reduce sequences into lower dimensional space, preserving only prominent data characteristics. Analysis is subsequently performed with these lower dimensionality transformations, enabling faster data comparison. Since SPDT methodologies such as the Fourier and wavelet transforms are applicable only to numerical sequences, nucleotide sequences must first be numerically transformed with one of several techniques including real number representations (Chakravarthy et al. 2004 ), complex number representations (Anastassiou 2001) , the DNA walk (Lobry 1996) , and the Voss method (Voss 1992) .