The phrase "alignment in color" is correct and usable in written English.
It can be used when discussing the consistency or matching of colors in design, art, or any visual context.
Example: "The alignment in color between the logo and the website background creates a cohesive brand identity."
Alternatives: "color coordination" or "color harmony".
36 An inbuilt dataset of 10 human OR sub-clusters is available in the TM-MOTIF package for users to assign new sequences to these clusters and to view the alignment in VIBGYOR coloring scheme, along with identified conserved motifs on the alignment.
The AB SOLiD alignment tool, mapreads, translates the reference sequence to dibase encoding (color space) and aligns reads in color space.
The SOLiD alignment software (Applied Biosystems, Foster City, CA) translates the reference sequence to di-base encoding ("color-space") and aligns the reads in color space, which avoids leading to the scale-up mismatches.
Hence, to facilitate the identification of regions of the model expected to be of high quality (i.e. highly conserved sequence alignment with no or few insertions and deletions), the structurally derived target-template alignment is shown in colors, highlighting regions of conservation between the modeled protein and the structure template (41).
Standard output formats have been made available including an HTML output generated with the Mview (19), a software that helps the visualization of the alignment in the browser by coloring identical sequences and showing the percentage identity between the sequences.
Short read alignments are shown in colors according to the respective genome, if they cannot be uniquely assigned to one unique parent they are shown in grey.
The visualization of web-based multiple sequence alignment results was implemented using the Jalview program [ 11], which provide a batch of tools to handle the alignment results and display the sequence features in color using the customized color schemes.
The best alignments, in which there are no gaps in the query or subject alignments are color coded in red; the next best alignments, that have subject gaps but no query gaps are coded in green; the third category, in which there are both query gaps and subject gaps are coded in blue and the poorest category, that contains query gaps as well as mismatches, is coded in black.
Best view in color Fig. 12 Example of 3D model alignment.
