The phrase "alignment that includes" is correct and usable in written English.
You can use it when discussing a type of alignment that encompasses specific elements or factors.
Example: "The project requires an alignment that includes all stakeholders to ensure successful implementation."
Alternatives: "alignment encompassing" or "alignment featuring".
In order to fill this gap, we propose in this work a new type of alignment, called syntenic global alignment, that includes three types of blocks: highly conserved blocks: blocks where regions with a high degree of similarity are aligned; conserved blocks: blocks where regions with a low degree of similarity are aligned; unconserved blocks: blocks where regions with no similarity are aligned.
Thus far, manual curation of a megabase-scale whole-genome multiple alignment that includes rearrangement and lateral gene transfer has proven too time-consuming and difficult.
We used a multiple sequence alignment that includes both the homeodomain and the additional conserved domains (Additional file 2).
2) Then for each gene, a profile hidden Markov model (HMM) [ 50] was built from a peptide sequence alignment that includes all orthologues found in the previous step.
The accD gene is too structurally divergent in S. noctiflora and S. conica to produce a useful alignment that includes both species.
Any alignment that includes sequence from the query outside of the embedded domain includes shuffled sequence that is not homologous to the library sequence.
Primers were designed on a multiple alignment that included all known LCDV genotypes.
Moreover, analysis of an alignment that included plant and stramenopile sequences indicated that new and more restrictive consensuses (GDNX7RX5P and EGDX8NX5(S/P)) could be defined for Imp1 and Imp2, respectively.
However, this may not be significant, given that the domain was defined on the basis of an alignment that included both archaeal and bacterial sequences.
A multiple sequence alignment that included all 12 nearly complete modern P. infestans mtDNA sequences plus all 13 herbaria samples was used as input.
Algorithms for sequence alignment that include the possibility of inversions have been proposed [ 55- 57], and they have the potential advantage of incorporating explicit penalties for inversion events.
