The phrase "a whole alignment" is correct and usable in written English.
It can be used when referring to a complete or comprehensive alignment of ideas, goals, or elements in a particular context.
Example: "The team worked tirelessly to achieve a whole alignment of their strategies before the project launch."
Alternatives: "complete alignment" or "full alignment".
A straightforward measure is percent identity (in which the number of identical nucleotides in the alignment is calculated as a proportion of whole alignment length).
These cases are largely an expression of comparisons between unaligned sequences; however, in some instances a part of the CDS or NCS aligned well but constituted only a minor fraction of the whole alignment, producing a value below 0.25.
The testing showed that there is a little saturation in the whole alignment for each of four analysed nucleotide data sets.
The knowledge of even one 3D protein structure in a given sequence alignment provides a powerful means to test the correctness of the whole alignment.
We performed a whole genome alignment of KN400 and PCA using Mauve (Darling et al., 2004) with a seed-weight of 15, a minimum island size of 50, and the Muscle 3.6 algorithm in order to check for completeness of all the homologous gene sequence.
Our second formulation allows a faster but lower-sensitivity solution for a whole genome alignment setting.
For a high resolution phylogeny within the Aquificales, we created a whole genome alignment using Pomago.
These three clusters were also apparent within a whole genome alignment (Additional file 2: Figure S1).
A whole genome alignment was produced by SNP-calling isolates, and regions that were recombinant were identified using the software package Gubbins (Croucher et al., 2014).
At first, a whole genome alignment of C. glutamicum ATCC 13032, C. efficiens YS-314 and C. diphteriae NCTC 13129 was created by MAUVE [ 85].
