To simulate a comminuted fracture, most studies were based on the creation of a gap (or segmental defect) at the osteotomy site, gap sizes varying up to 7 mm [ 6, 11].
Since each pair of neighboring ancestor nucleotides holds a potential insertion site (gap, "–") with an overall "gap:nongap" ratio of one, we assume a pentanomial distribution for general ancestor nucleotide states with sample space {–[0] A[1] T[2] C[3] G[4]} and normalized probability set (p0 = 1/2, p1 = p2 = p3 = p4 = 1/8).
Strain data, however, indicate the potential for significant repair site gapping under these physiologic loads.
Alignments showing more than 10% site gaps were also discarded from further analysis (Table S1).
The BiPad program performs multiple local alignment by entropy minimization and cyclic refinement using a stochastic greedy search strategy, and we used the following settings: left half-site, gap range lengths, right half-site, and the iteration cycles were set to 9, 0 or 1, 9, and 500, respectively.
The analysis was performed keeping the following cut-off values for prediction of target sites: gap open penalty 2.0, gap extend: 8.00, match score (S) ≥ 150.00, duplex free energy (Δ G) = −25.00 kcal/mol, and scaling parameter (w) = 3.00.
A phylogenetic tree was constructed based on an alignment of the nearly complete S-gene (4091 sites, gaps excluded), using MEGA5 software [ 22].
Our simulator and simulation results are additionally relevant for the analysis of other types of binary-coded data, such as the existence of homologues restriction sites, gaps, and introns, to name a few.
Only complete sites (no gap, no X) were used.
PCR was performed using immunoprecipitated DNA and promoter-specific primers flanking the p53 site for GAP-43 (M-Medical) and specific primers for GAPDH, used as housekeeping gene.
We also required that either all human sites were gaps or that all chimp sites were gaps within the indel sites in the human-chimpanzee alignment.
