The phrase "alignment parameters to" is correct and usable in written English.
It can be used in contexts related to settings, configurations, or specifications in technical or scientific discussions.
Example: "The software requires the alignment parameters to be adjusted for optimal performance."
Alternatives: "alignment settings for" or "configuration parameters for".
To see if performance could be improved for aDNA, we have modified the default alignment parameters to improve mapping sensitivity at acceptable run-times.
> -wrap-foot> Candidate male-biased EST and BAC sequences were further narrowed down by using relaxed alignment parameters to map the male and female Illumina data to the potential male-biased sequences with BlastN.
It performs sequence alignments using the program MAFFT [ 84] using different sets of alignment parameters to create three different alignments for each gene family and culls [ 85] alignment ambiguous regions.
In fact, by adjusting the BWA alignment parameters to reduce the gap opening and extension penalties (-b5 -q2 -r1 -z10) as recommended by the BWA author, the mappability substantially improves.
The BWA outputs using different parameter settings are highly similar to each other and to the Novoalign results; however, the Bowtie output revealed a number of miRNAs that had higher counts in comparison, despite setting alignment parameters to be similar to BWA (see Figure 1B).
Contigs were aligned with alignment parameters set to > 97% identity and > 40 nucleotides overlap using Sequencher (Gene Codes Corp., Ann Arbor, MI, USA).
We altered the alignment and alignment processing parameters to test the robustness of our analysis.
Alignment results were parsed to filter probes based on alignment parameters expected to influence hybridization strength.
The Blast output was subsequently parsed by custom scripts to filter probes based on alignment parameters expected to influence hybridization strength.
Alignment parameters needed to be more relaxed such that reads containing SNPs can still map to the consensus element and reads that contain adjacent non-repetitive genomic sequence may also map.
A noteworthy aside is that default alignment parameters often fail to align fungal repeats correctly due to complex internal repeat structures.
