All the alignments were carried out with a minimum alignment ratio of 0.93, and the minimum size of alignment of 20.
For an average neurite that is 225 μm in length for the HMA- co-HDDMA series, the neurite would travel an extra 30 μm of unaligned distance, that is, outgrowth that is not in the direction of the micropattern features, on the softest substrate with an alignment ratio of 1.32 compared to the stiffest substrate with a neurite alignment ratio of 1.18.
It is obvious that the alignment score Xa - Ya is lower than the alignment score Xa - Yb, while the alignment ratio of Xa - Ya is the higher of the two.
To estimate opened gaps in a structural alignment, the value of aligned ratio of a binding segment is measured.
As shown in Figure S3, the average difference of the alignment ratios calculated by this method for the two domains in a DSCO pair with <10% sequence identity was 9%.
Otherwise, its alignments are scored and the alignment ratios calculated.
Neurite alignment ratios (TL/AL) approaching unity indicate substantial alignment to the pattern direction along the entire the length of the neurite; higher ratios are indicative of greater wandering or random growth.
Co-orthologous genes matrix identified using the alignment ratio suggested close association of Citrus clementina, Citrus sinensis, and Citrus reticulata, as they belong to the same phylogenetic clade.
The user can choose strict or loose RScan parameters for balancing the computation time and more alignment results. 1 Mc: match-core; Id: identity; Ar: Alignment ratio. 2 ST: number of same type of ncRNA with the query; F5: number of same type ncRNA in first 5 hits.
However, as the alignment ratio cutoff decreased, the number of common global homologs in the testing set decreased much more rapidly than that of DSCO pairs (refer to Figure S1) and the remaining DSCO pairs maintained high scores that became relatively higher and higher than the scores of the partial and low-similarity homologs remaining in the testing set.
