All sequence data were downloaded from the NCBI databases and aligned using publicly available alignment software, MAFFT version 6 or 7 [ 32, 57] (http://mafft.cbrc.jp/alignment/server/) using our own-build Linux-based server.
The proposed machine learning framework is shown in Figure 2. As seen in the figure, the reads are generated by the sequencer from the donor genome and are aligned to the reference genome using an available alignment tool.
The total available alignment length of these overlapping sequences was 4,755,154 nucleotides.
Depending on the input alignment, this often limits the number of available alignment positions for the primer design considerably.
When using currently available alignment algorithms, there are several parameters that determine the outcome of the alignment process.
Strategy 2 uses all available alignment information (pairwise and multiple alignments) whereas strategy 3 does not use any alignment information in the actual motif discovery process.
