Sentence examples for between sequences were computed from inspiring English sources
Distances between sequences were computed by observed divergence.
In this method the distances between sequences were computed using the p-distance method and are in the units of the number of amino acid differences per site.
Specifically, 100 bootstrap replicates of the alignment were constructed using the SEQBOOT program, and the distances between sequences were computed by the PROTDIST program using the PAM substitution model.
For the bacterial microsymbionts, the average uncorrected p-distances (proportion of differences between sequences) were computed for each region and were found to be relatively small for dnaA (p = 0.0378), intermediate for glnA (p = 0.0625), and high for IGS nifD-K region (p = 0.0833).
Distances between orthologous coding sequences, and between paralogous sequences were computed from synonymous (Ks) and nonsynonymous sites (Ka) by the Nei-Gojobori method [ 33].
The number of base pairs available for comparison and the number that differed between two sequences were computed, together with the percentage identity between all gene segments within each strain pair, hence we computed the Hamming distance between each strain pair.
Numbers of synonymous (dS) and nonsynonymous (dN) nucleotide substitutions per site between homologous DNA sequences were computed by the modified Nei Gojobori method (Zhang et al. 1998).
Alignments between cDNA and UNIREF protein sequences were computed using BLASTX.
Similarities between each woman's state sequences were computed using the optimal matching (OM) distance algorithm implemented in TraMineR [ 12].
The global alignment between two sequences is computed by the Needleman-Wunsch algorithm implemented in the EMBOSS package [49], with following parameters: gap opening penalty = 10, gap extension penalty = 0.5, scoring matrix = BLOSUM62.
