The phrase "alignment to optimize" is correct and usable in written English.
It can be used in contexts where you are discussing the adjustment or arrangement of elements to improve efficiency or effectiveness.
Example: "We need to ensure alignment to optimize our workflow and enhance productivity."
Alternatives: "adjustment for improvement" or "coordination for enhancement."
Thus, our pipeline was specifically developed to reject these sequences before gene multi-alignment to optimize phylogenetic inference.
After the adapter trimming by cutadapt 1.8.1 (Martin 2011), the reads were aligned to the reference genome of Termitomyces sp. J132 (Poulsen et al. 2014), downloaded from http://gigadb.org/dataset/100056, by using Bowtie 2 with local alignment mode to optimize the mapability (Langmead and Salzberg 2012).
This alignment scheme aims to optimize the sum of the semi-global (overlap-detection) alignment scores on each side of a fixed split position in the transcript gap region.
Rigid alignment methods try to optimize a score that is usually dependent on the length and rmsd of the alignment.
Similar to SP3 and SP4, we used the Smith-Waterman local alignment algorithm [35] to optimize the score that matches the query profiles with template profiles based on Eq. (1) with the revised gaping method described above.
We use the Needleman-Wunsch global alignment algorithm [26] to optimize the matching score between the query sequence and template structure based on Eq. (1) with the position-dependent gap penalty model described above.
Local network alignment (LNA) aims to optimize similarity between local regions of different networks [ 10– 10].
Where necessary, multiple sequence alignments were manually adjusted to optimize the alignments.
Unlike other multi-genome comparative tools that display columns of aligning bases with gaps to optimize alignments, EvoPrinter displays, in a single uninterrupted view, DNA sequences that are either conserved, unique or uniquely shared, including single nucleotide polymorphisms (SNPs), as they exist in the genome or MGE of interest.
For this reason, we used an alignment of several experimental structures to optimize our alignments.
