Nucleotide sequences from the M, I and K domains were aligned with reference to the corresponding amino acid alignment using Clustal X [ 47] and appropriate settings (pairwise alignment parameters for gap opening 22.5 and for gap extend 0.45, multiple alignment parameters for gap opening 12.5 and for gap extend 0.25).
We developed an efficient computational procedure for integrating two PINs with reference to the global protein network alignment method in an attempt to obtain the integrated PIN [ 42].
To elucidate the migratory phases of CIL, we first analyzed the changes in acceleration throughout the response with reference to the time of microtubule alignment between colliding hemocytes, which we previously revealed is a hallmark of CIL that is associated with a change in hemocyte motility (Stramer et al., 2010).
Of the 306 CR, 77 cyt b, and 8 ND5 sequences, 122, 23, and 5 were judged to be authentic and reliable with clear locality information with reference to the original paper and preliminary alignment, respectively (Table 2).
The presence or absence of the established NAI resistance-associated mutations, R292K and E119V, was then determined by inspection of the resulting amino acid alignment, with reference to the influenza A/Syd/5/97 (H3NA) NA sequence, which was isolated before the licensing and widespread use of neuraminidase inhibitors that began after 1999/2000.
The quality of the impulsion was rated with reference to the take-off angle, body segments alignment and knee position of the free limb.
Amino acid sequences were aligned using ClustalX [ 52] then its nucleotide sequences were aligned with references to the amino acid sequences alignment using CodonAlign 2.0 [ 53]) and further edited manually.
A molecular replacement search model was subsequently created from the wheat structure using the program CHAINSAW [53], [54] with reference to an alignment of the wheat and pea sequences generated using the CLUSTALW server [55], [56].
These were designed with reference to an alignment of the known allele sequences for ovine DBR1 (figure 1).
The word template-based alignment was originally coined by Taylor Taylorr, 1986) with reference to sequence/structure alignments.
