The phrase "alignment secondary" is correct and usable in written English.
It can be used in contexts where you want to indicate that alignment is not the primary focus or consideration.
Example: "In this project, we will prioritize functionality, with alignment secondary to our main objectives."
Alternatives: "alignment is not primary" or "alignment is of lesser importance".
The detailed sequence alignment, secondary structures and domains of Pak2, PKA and Src are shown in Figure 2. The glycine-rich loop, catalytic loop, magnesium positioning loop, APE motif and F-helix are highly conserved in the alignment.
Alignment secondary structure predictions were performed with the JPred program [ 71].
Sequence alignment, secondary structure prediction, and tertiary structure prediction were used to design NCOA4 fragments for identification of the ferritin-binding domain.
Multiple sequence alignments were built using the Kalign [ 86] and MUSCLE [ 87] programs, followed by manual adjustments based on profile profile alignment, secondary structure prediction and structural alignments.
To model the N- and the C-terminal regions of PPLP2, AnDOM algorithm, two threading algorithms, multiple alignment secondary structure predictions and critically-reject-bad-structure predictions were used in the QUARK program (Xu and Zhang, 2012).
Multiple sequence alignments were built using the Kalign [ 153], MUSCLE [ 45] and PCMA [ 154] programs, followed by manual adjustments based on profile profile alignment, secondary structure prediction and structural alignments.
In combination with fold prediction and consistency checking (multiple sequence alignments, secondary structure prediction, and position analysis), repeat prediction with the new HHpred/COACH protocol dramatically improves prediction in the twilight zone of fold prediction methods, as well as the delineation of HEAT/ARM domain boundaries.
The website is easy to browse, and includes details of the associated gene as well as detailed graphical representations of a number of CNE features, including sequence alignments, secondary structures, and positional information.
Sequences encoding RNase P RNAs of various genomes have been determined and a database established [ 53], which consists of a compilation of ribonuclease P RNA sequences, sequence alignments, secondary structures and three-dimensional models.
In all cases, predictions and alignments yielded consistent results with respect to the sole alpha helix and five of the six β-strands of the PARP-1 catalytic domain (see additional files 3, 4, 5, 6, 7: "Multiple amino acid sequence alignments, secondary structure predictions and threading results for pART subgroups 1 5").
The alidot program [ 51, 52], finally, extracts local conserved structures given a sequence alignment and secondary structure predictions for each of the aligned sequences.
