Distinguishing between intra-genomic helitron families using time-frequency features and random forest approaches

Comparative genomic signature representations of the emerging COVID-19 coronavirus and other coronaviruses: High identity and possible recombination between Bat and Pangolin coronaviruses

“…The numerical genomic representation using coding methods is an important step to visualize and characterize the hidden information that can be contain in it, especially in this case where the nucleotide sequences do not have any continuously or homologous between them. Different coding techniques exist: the binary [20], the structural bending trinucleotide (PNUC) [21], the electron-ion interaction pseudopotential (EIIP) mapping [22], the FCGS [23][24][25], and so on. In addition, several signal processing techniques were applied with success to detect the relationship between sequences and detect some biological repetitive sequences, and so on.…”

“…Then, 1-D signals are generated by applying the FCGS order 2: FCGS 2 . This type of coding technique is based on the apparition's probability of two successive nucleotides in an entry sequence [23][24][25]. The probability (P 2_nuc ) of given L nucleotides in the sequence is as follows:…”

“…To reach this goal, we choose the wavelet transform as an analyzing technique which present the nucleotide signal into a nucleotide image. Our choice is based on the performance of the wavelet transform which have been especially used in data related to the biological domain [22,24,26,27].…”

Different genomic representations of novel pathogens base on signal processing algorithms: COVID-19 case study

“…Graphical signature representation is a very important step to know the variation between different genomic sequences [31,[34][35][36][37][38][39][40]. The major advantage of this step is being unworthy of any need for any previously biological knowledge.…”

New methodology for repetitive sequences identification in human X and Y chromosomes

“…Indeed even if the repetition pattern contains variations in nucleotide composition, this does not greatly impact the overall shape of the repetitive pattern at the level of DNA image. Furthermore, our choice for this method is reinforced by its performance in characterizing different classes of transposable elements [ 30 , 31 ]. For the wavelet analysis, we use the complex Morlet wavelet which is best suited to localize repetitive DNA in the time-frequency domain.…”