The phrase "a best alignment of" is not correct in standard written English.
It can be used when discussing the optimal arrangement or positioning of elements in a specific context, but it should be rephrased for clarity.
Example: "We need to find the best alignment of our resources to achieve maximum efficiency."
Alternatives: "the optimal alignment of" or "the ideal arrangement of".
Twenty-six (54%) of the non-conserved miRNAs had a best alignment to Arabidopsis sequences, of which two predicted target genes were annotated only as expressed sequences.
Taking this into account, the score of a best alignment ending in the first position of a possible exon (resp. intron) can only be calculated in the presence of the dinucleotides AG (resp. GT) in both sequences.
Consequently, the score of a best alignment ending in the first (resp. last) position of the searched gene can only be calculated in the presence of the codon ATG (resp. TAA, TAG, TGA) in both sequences.
Likewise, the score of a best alignment ending in an unconserved (intergenic) region cannot be calculated from the score of a best alignment ending in a conserved region (intron) of the two sequences.
Given this fact, the score of a best alignment ending in a conserved (intronic) region cannot be calculated from the score of a best alignment ending in an unconserved (intergenic) region of the input genomic sequences.
From the quality-filtered A. fragilis reads, we performed a nucleotide Blast of each A. fragilis read to the S. purpuratus GLEAN3 database, rejecting any alignments that had a best alignment score less than 100, had a second-best alignment score greater than 70% of the top hit (to reduce issues of paralogy), any frameshift gaps, or that were less than 99 bps in length.
The best alignment of a query in an utterance is defined as the one that minimizes the average distance in a warping path of the normalized cost matrix.
Our interest in this article is not the search process of Infernal, but how a parse is scored and the best alignment of string against model is selected.
The DTW search looks for the best alignment of the query and a partition of the normalized cost matrix corresponding to a speech segment.
The best alignment of the respective query sequences, with a BLAST similarity score above 100 and identity above 90%, was anchored on the genome sequence.
