Sequences were aligned using Clustal × version 1.83 [ 59] with default penalties for gap opening and gap extension, and alignments were visually verified.
Neurite extension and fiber alignment has been previously examined using PC12 cells.
For KS evaluation, pain, range of motion, anterior posterior and medio-lateral stability, flexion contracture, leg extension and varus valgus alignment were investigated.
We aligned all of the sequences using CLC Genomic Workbench software with the following parameters: gap open cost, 10; gap extension cost, 1; and alignment type, very accurate.
The program uses exact matching, clustering, and alignment extension strategies to create a dot plot based on the number of identical alignments between two genomes.
The program uses exact matching, clustering, and alignment extension strategies to create a dot plot based on the number of identical alignments between genomes.
According to Ariel et al. (2003) [ 7], the script adopts these parameters: e-value ≤1e-10 alignmentnmextensionsion)/ query length) ≥ 0.8.
As mentioned in the miRanda Algorithm section, the gap opening and extension costs, scoring matrices and alignment score update are different for the inside and outside seed regions.
A synteny plot was generated using the program NUCmer, which uses exact matching, clustering, and alignment extension strategies to create a dot plot based on the number of identical alignments between two genomes [ 29].
Markov clustering and subsequent filtering based on sequence identity and alignment extension allowed us to define 43,960 homologous families (supplementary fig. 2, Supplementary Material online), including 3,959 gene families containing four or more sequences.
