Sentence examples for optimize alignment from inspiring English sources
Reads of BAC pool rP were aligned using Mosaik to GenomeZipper sequence dataset with the aim to optimize alignment parameters.
In addition, we used the local alignment configuration of Bowtie2, which allows reads' end "trimming" to optimize alignment.
In order to optimize alignment parameters or measure the quality of alignments, a cost function was used which does not rely on any reference or ideal 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.
The model can optimize alignments in mountainous terrain or regions with very complex geography.
Alignment is a computationally intensive process, and many computer programs (e.g., BWA aligner [ Li and Durbin, 2009]) have been devised that implement and optimize alignments according to various measures of similarity.
In contrast to most comparative multi-sequence alignment tools (reviewed by [ 7]), which display columns of sequences that contain gaps to optimize alignments, the species-centric EvoPrint is a single uninterrupted sequence and thus displays more bases in a single view than is possible with conventional alignments.
We optimized alignment parameters (below), including the number of allowed mismatches (-v) and the number of reported mappings (-m or -a).
In order to optimize the alignment, we align the domains separately and then join the alignments.
The first intron of S7 gene were aligned with Clustal X [ 138], using default parameters, to optimize sequence alignment including gaps and aligned sequences were later checked by eye.
Also, although investigators are encouraged to perform similar types of experiments to optimize the alignment conditions for their region of interest, the kmer search and Needlema-Wunsch alignment approach was robust to perturbations in their settings.
