The trinucleotide frequencies were counted by moving the window one nucleotide at a time.
When a comparative sliding window for nucleotide diversity is applied on all aligned sequences or within each group, as shown in Figure 4, higher substitution rates are seen to be in the U3 region.
For this, ANACONDA 2.0 scanned full chromosome sequences starting at the first six nucleotides and moved the scanning window three nucleotides at each step.
We performed a visual inspection of the alignment using a sliding window 600 nucleotides in length to identify regions containing variable sites such as single-nucleotide polymorphisms (SNPs) and indels (Kumagai et al., 2010).
The number of period-10 occurrences in a window ±51 nucleotides from each motif/complement position was determined.
The ANACONDA 1.0 algorithm developed previously [20], [29] simulates the ribosome during decoding by reading Open Reading Frames (ORFs) sequences, starting at the AUG initiation codon and moving the reading window three nucleotides at a time (Figure 1A).
NCSF was used with a search window 20 nucleotides long and four measures of conservation: Shannon informational entropy [22], redundancy [23], 'average dominant base count' and 'sub-sequence variant counts'.
The authors also used the same size of window (203 nucleotides) and the same codification.
Coding sequences were read with a moving window 41-nucleotide in length.
The algorithm developed simulates the ribosome during decoding by reading Open Reading Frames (ORFs), from the ATG initiation codon, and moving the reading window three nucleotides at a time until a stop codon is encountered.
