The phrase "alignment to reference" is correct and usable in written English.
It can be used in contexts such as data analysis, bioinformatics, or any field where comparing or aligning data to a standard reference is necessary.
Example: "The software performs an alignment to reference to ensure that the genomic sequences are accurately compared."
Alternatives: "alignment with reference" or "reference alignment".
mRNA abundance is determined by sequencing either 3' end tags or random cDNA fragments (digital transcript expression, DTE), followed by read alignment to reference databases and calculation of aligned read frequencies.
Figure 4 Conformer alignment to reference shapes.
The alignment to reference sequence was performed using Sequencher 4.8 software.
Even in the case of a new organism without a preexisting reference sequence, this time frame would be enough to at least identify the pathogen at the genus and species level and possibly identify any virulence and antibiotic markers by alignment to reference databases.
MeDUSA utilized BWA (v0.5.8) [ 44] for alignment to reference genomes.
Another alternative to alignment to reference libraries is k-mer analysis.
The alignments to reference were parsed to count all inserted, deleted, substituted and unmapped bases.
Then for each query, it performs seeding, filtering and banded alignment to identify the alignments to reference sequences that meet user-defined cutoffs.
The latter case would require scaffolding to resolve based on alignments to reference transcripts, but was not conducted in these assemblies.
We assessed the quality of the alignments produced by DELTA-BLAST, BLASTP, and CS-BLAST by comparing these alignments to reference structure alignments, using two standard metrics – sensitivity and precision.
Although increasing the number of reads beyond 10% contributed little to finding novel hits to the local Arabidopsis data base, increasing the amount of data did help extend the existing contigs and generate longer alignments to reference genes.
