The phrase "alignment or alignment" is not correct and does not make sense in written English.
It seems to be a repetition without context, making it unclear when or how to use it.
Example: "We need to discuss the alignment or alignment of our strategies moving forward."
Alternatives: "alignment or adjustment" or "alignment or coordination".
If so, the best alignment or alignments are those with the lowest total score of mismatches and penalties on the two ends.
For a given read, our program is designed to report the 'best' alignment or alignments, those with the lowest score based on mismatches plus an opening gap penalty for an indel or a splice.
In a series of filtering steps, sequences were removed from the individual alignments or alignment slices if they are (a) shorter than 50 nt, or (b) contain more than 25% gap characters, or (c) have a base composition outside the definition range of RNAz (e.g. GC content > 0.75 or < 0.25).
In our view, the challenge of adequately visualizing such very large alignments, or alignments with a large divergence between species lies not in finding a visualization that shows every detail at maximum resolution, but rather in appropriate summarization and a (semi-automatic) focusing on the important events.
Therefore, there are eight possible combinations of specificity for alignment A, alignment B or the consensus (Fig. 1B).
Graph alignment adopts concepts from sequence alignment; the alignment scores are adjusted to reflect topological or relational information for the graphs.
a significant and unique sub-map alignment; an alignment labeled as non-significant and/or non-unique (which will be considered as a false alignment); or no feasible alignments found.
As is the case for sequence alignment, network alignment methods can produce both local and global alignments between two or more species.
Over two experiments we develop two instructional analogies using a combination of structural alignment, progressive alignment, and hierarchical alignment.
We define Impact as the normalized difference between Alignment and Alignment∗.
