In this formula, the identity t i of the true contigs i is calculated as the number of aligned bases over the length of the alignment.
Sequence identity was multiplied by the length of the alignment relative to the total protein length (≤1), which penalizes non-aligned regions.
Specifically, the standard Pearson correlation coefficient was calculated for each aligned pair of column vectors and summed over the length of the alignment to provide a raw score.
We call N the total length of the alignment covered by human and mouse ESEs, i.e., the number of aligned nucleotides labelled as H and M in Figure 8.
Other studies of brown bear have estimated various time to the most recent common ancestor (tMRCA) for other clades, in particular influenced by the length of the alignment (single mtDNA genes versus whole mitogenomes) and the method of calibration (e.g. tip-dating, fossil calibration 1,13,28.
Nucleotide similarity greater than 85% all over the complete length of the alignment was required to identify orthologous candidates (Supplementary Figure 1).
Static ground water table was not encountered in any of the trial pits dug for the collection of soil samples throughout the length of the alignment.
The scores were normalized by the length of the alignment.
The total length of the alignment was 6 kb and all genes had similar evolutionary rates.
Again, discrepancies between actual protein lengths and length of the alignment reflect the presence of indels.
Sequences were clustered if the identity was ≥95% (++ or +− strand) and the length of the alignment was ≥40 bp and ≥80% length of the shorter sequence.
