Given an alignment with N sequences, we had four different methods, "BEST", "SECOND BEST", "SHUFFLE" and "RANDOM", to generate another N-1 sequences (for details see Methods).
The algorithm, like PETfold is a maximum expected scoring approach that combines the evolutionary probabilities Prev of a consensus structure, σ, given an alignment, with the thermodynamic probabilities of the associated structures in each sequence.
Annotations were considered accurate when either BLAST search gave an alignment to a predicted protein with an E-value of < 1e-10 and a score of ≥ 200.
Given an alignment between a sequence with a known structure (Template) and a sequence of unknown structure (Target), the STRIKE score is estimated by projecting all the contacts measured on the template onto the target.
PAM2, a similar entropy matrix, gave an insignificant alignment with a score of 22.8 bits and an E-value of 0.43 for an overlap of only 6 amino acids.
Given an alignment, we generated all possible cyclic orderings and computed the fraction r of sites with q > 0.8 among all variable sites in the alignment.
Approximately 17% of the SNPs had flanking sequence data which gave a significant alignment with an annotated gene in the stickleback genome.
The single-stranded probabilities are as follows: (17) Given the structure σ on an alignment with m columns, the set of all single-stranded positions in the consensus structure is denoted as ss = { i ∉ σ|1 ≤ i ≤ m}.
Whenever the highest scoring alignment for a given RefSeq transcript was derived from an alignment with an AspicDB prediction (and there was no RefSeq transcript producing an alignment with equal score), then the match type assignment was adjusted according to the one produced by the new alignment.
The simulation of vehicle dynamics is based on the essential train dynamics equations in Hay [25], which divide the train operation between each pair of neighboring stations into acceleration, cruising, and braking stages, and then calculates train energy consumption and travel time along a given track alignment with an iterative process [21].
