Sentence examples for alignment and removal from inspiring English sources
Following alignment and removal of intronic sequence, we used the 48 alleles obtained from each gene to perform MacDonald-Kreitman tests as implemented in DNAsp.
After alignment and removal of the sites with gaps, a total of 650 amino acid sites are included in the analysis.
Those clusters that contained at least one species in addition to L. hesperus, L. geometricus, S. grossa, and tick after alignment and removal of short sequences (described in detail below) formed the arachnid gene clusters (fig. 2 A).
We included 100 representative species (103 accessions; online Additional file 1: Voucher) in the combined sequence data set that contained 2024 nucleotide positions after alignment and removal of ambiguous sites.
After alignment, filtering, and removal of CpG-prone sites, the data set could broadly be defined as composed of 2.97 million 0-fold degenerate sites, 0.34 million 4-fold degenerate sites, 7.94 million bp of intronic AR, and 58.19 million bp of non-AR intron sequence.
Multiple sequence alignment and gap removal were carried out to extract homologous regions of sequences from the four subfamilies of terpenoid synthases.
After a manual curation of the alignments and the removal of false positives, we obtained two verified helitron families named HELPO1 and HELPO2.
Such steps include local realignment, base quality score recalibration, base alignment quality recalibration (BAQ), and removal of duplicate reads.
Alignment of individual genes and removal of unalignable characters was performed as described in Fučíková et al. [ 7].
This initial alignment allowed for identification and removal of classes lacking any identifiable features (generally false positive particle picks) or clearly identifiable as a non-ribosomal E. coli complex.
The exome analysis pipeline is perhaps the most time-intensive pipeline with three long processes read alignment, duplicate removal, and variant calling.
