The phrase "alignment to regions" is correct and usable in written English.
It can be used in contexts where you are discussing how something corresponds or fits with specific geographical or conceptual areas.
Example: "The project's success depends on the alignment to regions that have the highest demand for our services."
Alternatives: "correspondence with areas" or "conformity to regions".
Non-homologous alignments to regions with no annotated Pfam domains were used as queries in reciprocal PSI-BLAST searches for three iterations.
We only considered alignments to regions of high quality sequence and that had >95% identity to the query, ignoring cases where the Ensembl model itself was from a region of poor sequence quality (see Methods for details).
BLAT connects these matches because its default parameter settings allow alignments adjacent to a masked region to be extended into the masked sequence while SSAHA and MegaBLAST, whose default settings do not allow alignment to masked regions (see Methods), show the masked region as a gap.
Limiting read alignment to affected regions of the assembly Since only a small portion of the assembly is affected in each step, we can keep most alignments from the previous iterations and only align reads to the regions that changed.
However, there are several limitations inherent to the alignment process, including alignment to repetitive regions, absent or misassembled sequence in the reference genome, and individual genetic divergence between the subject organism's genome and the reference genome [ 1].
Partially-mapped reads are defined as high-quality full length (76 bp) reads where the best alignment to targeted regions is a perfect match less than 76 bases in length.
This heuristic vastly improves the overall speed by restricting the expensive alignment process to regions containing these short exact matches.
Alignment to the region from O. kenojei showed two large blocks of 473 and 486 bp each with 85 and 75% identity, respectively.
Bismark fully bisulfite converts sequence reads and maps each to bisulfite converted versions of the reference genome, with only reads producing a unique best alignment to a region being kept.
While multiple species are used for comparison, a sequence block can be assigned a high MCS score even if not all the compared species show alignment to the region.
