The phrase "alignment we used" is correct and usable in written English.
It can be used when referring to a specific method or approach that was previously applied in a context, such as a project or analysis.
Example: "The results of the study were influenced by the alignment we used during the data collection phase."
Alternatives: "the alignment we applied" or "the alignment we implemented".
For sequence alignment we used RSEM, which aligns reads to known isoforms and then calculates gene expression as the sum of isoform expression for a given gene, assigning ambiguous reads to multiple isoforms using a maximum likelihood statistical model [ 25].
To align a group of sequences to a reference alignment, we used the "--add" option of MAFFT [ 94].
We used ClustalW with default parameters and gapopen = 0.0 to align the sequences shown in the Figure 2. Note that for the alignment, we used only the β-strand-rich region (β-barrel domain), positions 90 220.
For alignment, we used the default settings and the automatic optimization option in the online version of MAFFT95.
To define the varus or valgus alignment we used a mechanical tibial femoral angle which was formed by the line joining the center of the femoral head to the center of the knee joint and a second line from the center of the knee joint to center of the ankle joint.
For each combination of paired genomes, rather than attempt alignment, we used the portable implementation of tblastx [29] available in the NCBI Blast distribution (http://www.ncbi.nlm.nih.gov/blast/download.shtml).shtml
For global alignment, we use a graph-based approach making use of the same error metric and iteratively refine the complete vehicle trajectory.
As a performance measure of the alignment we use the average of the absolute alignment errors in seconds at the beginning and at the end of each lyric line.
Test data for alignment: We use the following three datasets to test the alignment accuracy of our method.
To bring models into further alignment, we use a Uniform (−100, 100) distribution over virus locations and serum locations.
When evaluating the amount of sequence data that should be used within NCF when generating an alignment, we use protein sequence similarity data.
