The phrase "alignments were compared with" is correct and usable in written English.
It can be used in contexts where you are discussing the comparison of different alignments, such as in scientific research, data analysis, or any field that involves comparing sets of information.
Example: "In our study, the alignments were compared with those from previous research to identify any significant differences."
Alternatives: "alignments were contrasted with" or "alignments were evaluated against".
The Viterbi alignments were compared with Clustal alignments (not shown).
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 difference between the immediate postoperative frontal plane radiographic alignments was compared with the preoperative deformity, and reevaluated after at least 1 year of weight-bearing function.
The trees produced with this trimmed alignment were compared with the set of trees produced from the alignment of the mouse sequences to their respective full-length proteins.
The tree topologies derived from the nucleotide data sets (each single locus and the concatenated alignment) were compared with tree topologies from the concatenated sequences of four genomic regions (b-tubulin elongation factor 1-α pPF_018 and pPF_076) sequenced previously [ 14] using the approximately unbiased (AU) and the weighted Shimodaira and Hasegawa (WSH) tests [ 29].
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).
