The phrase "alignment largely" is correct and usable in written English.
It can be used when discussing the extent or degree to which something is aligned or in agreement with another thing.
Example: "The alignment largely reflects the values and goals of the organization."
Alternatives: "alignment primarily" or "alignment mostly".
This strongly indicated that the reliability of 2-mismatch read alignment largely depended on the corresponding MMES score, i.e. those with large MMES score were more likely to be real ones while those with small MMES score were non-specific mapping artifacts.
Rail authority spokeswoman Rachel Wall said officials rejected the alignment largely because of concerns about curves slowing the high-speed train, as well as noise and other effects on cities along the corridor.
It has been previously demonstrated that GSK3 inhibitor-treated cells delay chromosomal alignment largely due to their inability to perfectly bi-orient all their chromosomes [33].
In this way alignments spanning short repeats were not penalized, but alignments largely composed of likely repeats were removed.
Secondly, BWA-SW only reports alignments largely non-overlapping on the query sequence instead of giving all the significant local alignments.
Fourthly, BWA-SW only reports alignments largely non-overlapping on the query sequence, while BWT-SW, like BLAST, reports all statistically significant alignments.
Because we only retain alignments largely non-overlapping on the query sequence, we might as well discard seeds that do not contribute to the final alignments.
In the case of Sma3s, the effect of the BLAST search is especially important given that Sma3s was able to annotate 90% of array sequences with BLAST alignments, largely due to the novel M3 module (Table 2).
Route 403's previous alignment was largely unchanged during the construction of the Quonset Freeway; only the interchanges with Routes 4 and 402 in East Greenwich and with US 1 in North Kingstown were altered significantly.
Importantly, the sequence region defined as the crotonase domain by a hidden Markov model (HMM) and the region covered by the BLAST alignment are largely overlapping; see Fig. 5D for an illustration of selected alignments used to define edges from the full-length crotonase network.
Since the alignment score largely depends on the protein length, we used the percentage identity for protein sequences, instead of the alignment scores.
