FP alignments were assigned to specific P site nucleotides by using the position and total length of each alignment, calibrated from FPs at the beginning and the end of CDSes.
Alignments were assigned to genomic coordinates as follows.
Each edge will therefore have two alignment scores assigned to it, AS seq (for sequence-based alignment) and AS func (for function-based alignment).
Segments of the alignment were assigned to structural motifs based on the KcsA structure.
The 240 experimental stimuli were gated, with the construction of the gating materials controlled by the alignment point assigned to each item.
In step 2, we define a partitioning scheme in which all sites in the alignment are assigned to a single subset, and we then select a best-fit model of molecular evolution for this subset.
Furthermore, we also describe a new barhl paralog in medaka which, based on protein alignment, could be assigned to the Barhl2 group.
Each column of the sequence alignment is then assigned to the clique containing the maximal number of sequences with non-gap characters in the column.
After manual inspection of the alignments, several genes initially assigned to the taxonomic categories were moved to the correct classification.
The only exceptions to this was in cases where two stickleback linkage groups showed identical numbers of RAD loci alignments, then both were assigned to that Atlantic salmon linkage group.
By comparing the e-value ratio (virus/fungi or virus/plant) of all proxy-reference genome alignments, 10 contigs were assigned to pea and 9 contigs were assigned to S. sclerotiorum based on an e-value ratio >1e, 30 contigs were difficult to distinguish, with e-value ratios between 1e-20 and 1e.
