Sentence examples for by aligning the reference from inspiring English sources

The primers were designed by aligning the reference genomes for the two species using the fungal alignment viewer provided by the Saccharomyces Genome Database [ 27].

Downstream breakpoints were determined by aligning the reference sequence with the reverse complements of the sequences generated using the reverse primers.

The upstream sequence breakpoints for each deletion were determined by aligning the reference sequence with the sequences generated using the forward primers in the sequencing reaction.

For each potentially amplifiable nuclear genome region, the percentage similarity to modern mtDNA was assessed by aligning the NCBI reference sequence to the rCRS in Sequencher version 4.8 (Gene Codes Corporation, Ann Arbor, MI).

Identification of regions in the reference genome not covered by reads was obtained by aligning the reads against the reference genome using the following two procedures: a) Tmap (as described above), SAMtools, and a custom script to identify regions with zero coverage and, b) CLC workbench (with 80% identity and 50% length fraction).

The next was to figure out the conformational change of Lec domain using the root of mean standard deviation (RMSD) of entire Lec domain or of specific regions, or the geometric center displacement of a residue by aligning the target to reference Lec domain, as well as the distance between specific residues.

We estimated the average error rate of filter-passed V1-2 data using 27Fmod-338R by aligning the V1-2 and reference 16S sequences of bacterial strains used in the two mock communities.

Intron and exon positions were determined by aligning the sequences with the reference sequences of each gene as follows: ACT1 (GenBank Accession No. U10867), URA5 (GenBank Accession No. AF032436), PLB1 (GenBank Accession No. AF223383), IDE (GenBank Accession No. XM568105).

Relative TMD positions were obtained by aligning the orthologs to the reference proteins using MUSCLE (Edgar, 2004).

Further images were then captured by aligning the dishes with the reference point made at time 0 h, and a second image acquired.

SNPs and INDELs of the wt strains obtained from the alignment with the GenBank reference genome were subtracted from those found by aligning the mutant strain with the reference.