The phrase "alignment inspection" is correct and usable in written English.
It can be used in contexts related to quality control, engineering, or manufacturing, where checking the alignment of components or systems is necessary.
Example: "Before finalizing the assembly, we need to conduct an alignment inspection to ensure everything is properly aligned."
Alternatives: "alignment check" or "alignment assessment".
Here, two groups of proteins, i.e. two mammalian proteins that are clearly globally similar to each other, and two nematode proteins that are clearly globally similar to each other based on alignment inspection, are being compared.
As an assessment of similarity search hits only by E value, bit score or alignment inspection can be challenging in the twilight zone [7], such a visualization can often help to sort out difficult cases.
Usually, regions of ambiguous alignment (RAA) are detected by alignment inspection and then discarded.
We used covariance model approaches, alignment inspection and synteny to exhaustively identify miR-100/10 family homologues in representative sequenced genomes (supplementary Fig S1 online).
An iterative procedure of HMMER search, alignment, manual inspection, and editing allowed us to construct full gene alignments, with annotated intron boundaries and BPs.
The X-box motifs, which are typically 14-mer DNA sequences, were initially identified as a result of alignment and inspection of the promoter regions of major histocompatibility complex (MHC) class II genes for conserved DNA elements [ 2, 3].
As a consequence, all alignments require inspection and interpretation, and often adjustment by hand, in order to produce an alignment that best represents the biological context of the sequences.
All default parameters were used in PAL2NAL and CLUSTAL W with the option SLO W/ACCURATEselected for CLUSTAL W alignments. Visual inspection confirmed an adequate alignment.
These sequences were then compared to known H5N1 sequences by alignment and visual inspection.
The IGV viewer is integrated into ClinLabGeneticist to display sequence alignment for visual inspection of variants.
Exons were identified by alignment and manual inspection (Table 2, 3).
