The phrase "alignment of reference" is correct and usable in written English.
It can be used in contexts where you are discussing the coordination or agreement of different sources or points of view.
Example: "The alignment of reference among the various studies ensures a comprehensive understanding of the topic."
Alternatives: "coordination of sources" or "congruence of references".
It is based on a preprocessing consisting in spatial and temporal alignment of reference and impaired sequences, region extractions, gain, and offset correction.
We apply standard and placement-type phylogenetic algorithms (see below) to the resulting alignment of reference sequences and reads.
Whole-genome alignment of reference genomes and core genome identification with Spine can be time-consuming with standard computer resources.
Extension of existing alignments with new sequences avoids these problems and guarantees that the relative alignment of reference sequences is not changed.
The NCBI refseq database and Swiss-prot provided an excellent resource for the C2H2 ZNF protein sequences used to generate HMM profiles after alignment of reference sequences.
Genome annotations of newly sequenced species initially rely primarily on ab initio gene predictions and alignment of reference transcripts of related species; however, the quality of gene models is greatly improved when incorporating same species transcriptomic sequencing [ 4].
In order to retain intronic sequences conserved among the species in each of the four groups, but not conserved between the groups, we removed ECRs that are found in orthologous introns as well as in any of the pairwise alignments of reference genomes; a minimum overlap of one base pair was used as a criterion for removal.
However, as we did not obtain PCR amplicons for every gene in every Arabidopsis lyrata accession, these were only tested across one to seven additional accessions (see Additional file 10 for predicted gene models and alignments of reference genome ORFs with ORFs from our de novo sequencing) and therefore SNPs in other accessions not sequenced may possibly exist.
If it is found to be contained in one of them, the candidate sequence is aligned by simply copying the matching part of the alignment of the reference sequence.
By decreasing the gap penalty between the two haplotypes, we created a single alignment of the reference region around gene GB45615 that included the reads formerly aligned to GB49510 to analyze the insertions and deletions.
This trivial transformation, while specific to alignment of a reference conformer, when applied, can yield a relatively accurate shape overlay between the query and database conformers without the need to perform the conformer overlay alignment optimization.
