It eliminates variants with no effect within a given region, separately analyzes positively- and negatively-associated RVs, and allows the adjustment for common variants and covariates.
Therefore, we analyzed positively selected amino acid sites of SmWRKYs using the improved branch-site model [ 72].
In the following section, we have analyzed the positively selected sites for those genes with evidence of lineage-specific positive selection in the context of their potential functional relevance for those genes.
We further employed the CODEML in PAML 4.0 to analyze the positively selected codons in each group.
We focused on Category 5 (Gene Ontology, GO) and analyzed genes positively correlated with aging (i.e. greater age = greater expression) and genes negatively correlated with aging (i.e. lesser age = greater expression) separately.
In analyzing cells positively transfected for tagYFP, we set a gate based on untransfected cells (Supporting Information Figure 4).
From the 11 protein bands analyzed, we positively identified 17 insect-derived proteins (Tables 2 and 3).
Per specimen 25 high-power-fields (HPF) were analyzed and positively stained cells were counted and given as number per HPF.
For example, neutral and basic glycosylated-peptides may be analyzed under positively charged ions mode, while acidic glycoconjugates (sialic acid and sulfate containing) tend to be detected more effectively as negatively charged [ 50].
In CV2, the difference in prediction accuracy between these two methods was low when the pairs of environments analyzed were positively correlated (e.g., in W1, environments 0iBN and 2iBN; see Table 9) and large, and in favor of the M×E model, when the set of environments analyzed were negatively correlated (e.g., in W3, in the joint analysis of 0iFN and 5iBN).
Therefore we can also address if the first 39 and last 33 amino acid positions of the Maloideae S-RNase protein, not analyzed before, harbor positively selected amino acid sites.
