The phrase "alignment using a" is correct and usable in written English.
It can be used in contexts where you are discussing the method or process of aligning something with the aid of a specific tool or technique.
Example: "The team focused on alignment using a new software tool to improve project coordination."
Alternatives: "alignment through a" or "alignment with a".
Third, unaligned sequences could then be aligned to the reference alignment using a variety of parameters.
In this article, we present a new paradigm for the alignment of environmental sequencing reads called PAUDA, an acronym for 'protein alignment using a DNA aligner'.
This was done by performing a read-to-contig alignment using a fast short read aligner.
A local alignment using a sliding window principle was used to align the TREs identified in mice to the promoter regions of the corresponding orthologous genes in rats and humans.
The fixed-column constraint necessary to allow concatenation of the individually aligned sequences into a joint MSA is maintained during DP alignment using a further modification of the Needleman Wunsch algorithm.
To evaluate the long-term effectiveness of improved ocular alignment using a suture/T-plate anchoring platform system.
The transcriptions of recordings were available and could be used for VAD through forced alignment using an automatic speech recognition system.
Alignments of sequences were obtained using CLUSTAL-W with default settings in place and EMBOSS pairwise global alignment using an implementation of the Needleman-Wunsch algorithm [52].
The two family alignments were aligned using a structural alignment of the two protein structures.
The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels.
We aligned these sequence sets and validated the alignments using a pattern-centric objective function [31].
