The phrase "actual alignment" is correct and usable in written English.
It can be used in contexts where you are discussing the precise positioning or arrangement of elements, often in technical or analytical discussions.
Example: "The actual alignment of the components was crucial for the success of the project."
Alternatives: "true alignment" or "correct alignment".
But the most compelling finding concerns the actual alignment of fortunes of managers and shareholders.
DALI's actual alignment process requires a similarity search after the two proteins' distance matrices are built; this is normally conducted via a series of overlapping submatrices of size 6x6.
Although specific details are lacking, the aligner uses a suffix tree to find related reference sequences and that the actual alignment step uses multiple reference sequences and secondary structure information to carryout the alignment.
This formula facilitates the calculations without computation of the actual alignment.
Therefore, regardless of the actual alignment there must be a 4 residue insertion somewhere in EF-2 of the Eukaryotes and Archaea.
We evaluate the overall CPU time used by the algorithms to fit the scoring parameters and to perform the actual alignment.
A good synthetic dataset should reproduce empirically-observed features of actual alignments, including gap (indel) structures and local correlations between nucleotides, both of which locally deplete the information content of an alignment and can elevate false-positive rates.
For each length, we tabulated the number of perfectly conserved sequences from the simulation and compared it to the observed number of segments in the actual alignments (Figure 2).
In actual alignments, signals such as TSRs, TG-CA box and flanking strings might be placed at incorrect positions by alignment algorithm.
Obtaining the actual alignments corresponding to occurrences with right end j and recovering the left end of the occurrence requires a traceback procedure through the dynamic programming matrices.
Similarity-based approaches are robust and are observed to have high binning accuracy since they infer taxonomic assignments by analyzing actual alignments obtained in the BLAST output.
