The phrase "alignment we created" is correct and usable in written English.
It can be used when referring to a specific alignment or agreement that has been established or developed by a group or individual.
Example: "The alignment we created during the workshop has significantly improved our team's collaboration."
Alternatives: "the alignment we established" or "the alignment we formed".
Based on the alignment we created multiple phylogenomic trees (maximum parsimony, minimum evolution, neighbor joining) including 100 bootstrap replicates.
To visualize a SuperGenome alignment, we created GenomeRing, an interactive circular visualization and integrated it into our visual analytics software M ayday (Battke et al., 2010).
Using these alignments, we created ACT-Graphs for all the known genes.
By using this repeat masked noncoding human marmoset and mouse rat pairwise alignments, we created 100-bp sliding windows, which have no gaps from nonrepetitive alignments, with a step size of 25 bp.
To further test the alignment procedure we created virtual 'ground truth trajectories' from which we generated sets of virtual trajectories by adding different levels of random noise.
To represent the kinome sequence alignment in ProKinO, we created two additional properties in these instances: hasPKAStartLocation and hasPKAEndLocation; these store the aligned start and end residue positions with respect to PKA.
To calculate false discovery rate (FDR) of term alignment, we first create n ontologies with the same structure as the inferred ontology O i but with all gene labels randomly permuted.
To test the robustness of KalignP on the alignment of TM proteins, we created another reference dataset PfamA-mem which was derived from Pfam-A (version 24.0) seed alignments and filtered by matching the key word 'transmembrane' in the 'DE' record.
We created alignments for MAPP using three different methods.
To analyze the effect of the evolutionary divergence on prediction accuracy, we created alignments in which the minimum pairwise identity to the seed was restricted.
To examine whether both alleles at heterozygous sites were equally considered during alignments, we also created a "complement" reference sequence by swapping the allele at each heterozygous site in the initial custom reference with the alternate allele from the input file.
