The phrase "alignment to define" is correct and usable in written English.
It can be used in contexts where you are discussing the process of aligning elements or ideas in order to establish a clear definition or understanding.
Example: "We need to achieve alignment to define our project goals clearly."
Alternatives: "alignment for clarification" or "alignment to establish".
We have used the 17-way multiple gene order alignment to define conserved syntenic regions over multiple species (CSMs) and complementary evolutionary breakpoint regions (EBRs).
C.elegans gene annotations from Wormbase release 140 [ 16] were projected onto the whole genome alignment to define upstream regions.
To transfer this information from other closely related species to the species of interest, we use protein sequence alignment to define a measure of similarity between the proteins from the two species.
rRNAs were identified using BLASTN [14] alignment to defined rRNAs from the EMBL nucleotide database; tRNAs were identified using tRNAscan-SE [24]; stable RNAs were identified using Rfam [25].
rRNAs were identified using BLASTN [ 116] alignment to defined rRNAs from the EMBL nucleotide database; tRNAs were identified using tRNAscan-SE [ 122]; stable RNAs were identified using Rfam [ 123].
rRNAs were identified using BLASTn (Altschul et al. 1990) alignment to defined rRNAs from the EMBL nucleotide database; transfer RNAs (tRNAs) were identified using tRNAscan (Lowe and Eddy 1997); stable RNAs were identified using Rfam (Griffiths-Jones et al. 2003).
Protein motifs were identified using Pfam [ 85] and Prosite [ 86], transmembrane domains were identified with TMHMM [ 87], and signal sequences were identified with SignalP version 2.0 [ 88]. rRNAs were identified using BLASTN [ 83] alignment to defined rRNAs from the EMBL nucleotide database; tRNAs were identified using tRNAscan-SE [ 89]; non-coding RNA (ncRNA) were identified using Rfam [ 90].
Briefly, the method uses publicly-available genomic alignments to define probe set interrogation regions within the genomic sequence.
Later, methods that are more sophisticated have been developed with given pairwise or multiple sequence alignments to define conservation regions [ 4- 6].
When multiple contigs/singletons match the same database sequence, LANE runner 2.0 performs Clustal Omega (Sievers and Higgins 2014) alignments to define the relative positions of the input sequences and assembles them into a "one-to-many consensus".
Since the quality of homology based fold prediction is proportional to the degree of sequence identity and alignment coverage between template and the target proteins [ 41], we generated three different test cases based on the alignment criteria to define the homology.
