The phrase "alignment reference" is correct and usable in written English.
It can be used in contexts where you are discussing a point of reference for alignment, such as in design, engineering, or project management.
Example: "Before proceeding with the adjustments, please ensure that the alignment reference is properly set to avoid any discrepancies."
Alternatives: "alignment guide" or "reference point for alignment".
This fact leads to an enlarged alignment reference space.
For deletions, the build-up of the split-read alignment reference demands a simple extraction of the paired-end SV interval from the genome.
These sequences were used to construct a reference upon which subsequent assembly was based (see section: Assembly and alignment; reference available in Dryad accompanying this paper).
RefAligner assumes the alignment reference has the error profile of in silico maps and the query has the error profile of consensus genome maps.
HATS-PR represents, to our knowledge, the first usage of a guide tree in a spectral alignment method, which removes the requirement that all compounds be present in a single spectrum selected as the alignment reference.
However, a more focused approach by (1) utilizing the C-terminus conserved region as an alignment reference point for all vsps, and (2) gradually adding additional, longer upstream sequences allowed us to identify minor clades of vsps for running alignments, generating trees, and testing for evidence of recombination.
Many motif-finding methods would benefit from the alignment referencing provided by the HMM's scaffolding of annotation across coding and noncoding regions.
The application processes the reads produced by the sequencer in the following manner: quality control, genomic alignments, reference and novel transcriptomic junction alignments, alignment cleanup, identification of genomic features per sample, and summary of data across samples.
We encourage using the 'big' standards for data exchange always when applicable, and BioXSD for the exchange of common, everyday bioinformatics data like sequences, alignments, references and unified generic sequence annotations.
The regions were aligned using the ClustalW alignment program (reference) with the default parameters.
Figure 4 Conformer alignment to reference shapes.
