The phrase "alignments was compared with" is not correct due to subject-verb agreement; it should be "alignments were compared with." You can use it when discussing a comparison between different alignments in a specific context, such as scientific research or data analysis.
Example: "In the study, the alignments were compared with previous findings to determine consistency."
Alternatives: "alignments were contrasted with" or "alignments were evaluated against".
After downloading the BAM files for analysis, MeDIP alignments were compared with control samples using Cuffdiff 2.0.2 as previously described [ 64, 63].
Sequence alignments were compared with the original sequence of the NOS3 gene [GenBank: NM348236], and all SNPs were positioned in the sequence, and their mutation classifications were assigned (Table 1).
Amplified DNA was sequenced directly by GENEWIZ, Inc. (Research Triangle Park, NC, USA), and alignments were compared with those of GenBank sequences by using AlignX software (Vector NTI Advance version 11.5; Invitrogen, Carlsbad, CA, USA).
The initial sequence alignment was compared with the initial structure alignment, and adjusted in Jalview to ensure the sequences with unknown structures were properly aligned with the known structures.
Every gene was blasted against the nr database from NCBI and every orthologous group alignment was compared with the same database by Psi-BLAST (Altschul et al. 1997).
The ln-likelihood of the species phylogeny for each alignment was compared with all possible GC-type gene trees (table 1), using a codon model of evolution (see Methods).
The result of this alignment was compared with the reference standard of manually selecting matching slices, which was performed by a trained researcher (J.vT).
The sequence that had the longest local alignment was compared with the sequence with the next longest alignment, and the common aligned region was retained, potentially trimming one or both ends of either sequence.
In addition, the phylogenetic distribution of each putative ncRNA was examined, and each alignment was compared with existing RNA-seq data to identify regions likely to be within the rpsO transcript.
