Amino acids were iteratively assigned to template positions randomly, within hydrophobic groups.
Strand transfer is unique; the DNA strand being made by viral reverse transcriptase (RT) is moved from one RNA template position to another.
(3) Randomly select N t template positions from q 1, θ t, σ t x, y using a secret key KEY t 2, which is denoted as PS = {(x i, y i ), i = 1, 2, …,N t }.
For each parameter pair, compute the candidate template position as: x ′ i = round ( ( x i − cx cos ϕ + ( y i − cy ) sin ϕ ) / σ + cx ) y ′ i = round ( ( y i − cy cos ϕ − ( x i − cx ) sin ϕ ) / σ + cy ), (41).
The +2 position is also the first template position downstream from the bound dNTP in the +1 dNTPRTP/T complex.
UV-induced cross-linking between RT and the DNA template strand was most efficient when a bromodeoxyuridine residue was placed in the +2 position (the first template position downstream from the incoming dNTP).
In UV photo-cross-linking studies carried out with Klenow fragment of E. coli DNA polymerase (KF), Y771 was identified as the major cross-linking target in ternary complexes with BrdU at the +2 or +3 template position [31] or with a TT sequence at positions +2 and +3 in the template [32].
The alignment score of SP5 for aligning query position i with the template
Template positions corresponding to pause sites are indicated.
Suppose that two adjacent sequence positions are aligned to two template positions j1 and j2 (j2> j1+1), respectively.
