The phrase "alignment cover" is correct and usable in written English.
It can be used in contexts related to mechanics, engineering, or design, where it refers to a component that ensures proper alignment of parts.
Example: "Before starting the assembly, make sure the alignment cover is securely in place to avoid any misalignment during operation."
Alternatives: "alignment shield" or "alignment casing".
We set the parameters to utilize the BLOSUM62 matrix and a minimum bit score of 30, and we required that the BLAST alignment cover at least 50% of both proteins.
The other set was based on a stringent coverage criterion, requiring that the alignment cover 80% of the coding sequence.
One set was based on a relaxed coverage criterion, requiring that the alignment cover at least 50% of the coding sequence.
We set the parameters to use the BLOSUM62 matrix and a minimum bit score of 30, and we required that the alignment cover at least 50% of both proteins.
In such graphs, the nodes represent the objects to be compared (here ciliate V4 sequences), each pair being linked by an edge if there is significant similarity between the two corresponding nodes (here a minimum % identity (%ID), E-value, length, and alignment cover spanning over the two sequences).
Protein sequences were considered paralogous if their alignment had an E-value less than or equal to 1e-5 and the alignment covered 70% or more of one of the aligned proteins.
Gene duplication events were defined based on the following three criteria: (a) the alignment covered >80%% of the longer gene; (b) the aligned region had an identity >80%%; and (c) only one duplication event was counted for the tightly linked genes [ 38, 60].
We call N the total length of the alignment covered by human and mouse ESEs, i.e., the number of aligned nucleotides labelled as H and M in Figure 8.
the percentage of the alignment covered by the blocks.
Our alignment covers approximately 60% of the A. nidulans genome; hence we are only scanning 60% of the genome in our study.
A hit was considered significant if the alignment covered at least 50% of both sequences, and contained at least 50% identities [71].
