Sentence examples for by alignment with reference from inspiring English sources
Single-nucleotide polymorphisms (SNPs) were determined by alignment with reference strains (M. tuberculosis H37Rv accession no. NC_000962.3 or M. canettii cluster A Percy3 [STB-D CIPT140060008 accession no. NC_019950.1]) as described (7 ; Technical Appendix 1).
Obtained sequences were examined for the presence of mutations by alignment with reference DNA sequence (GenBank U14680 for BRCA1; GenBank U43746 for BRCA2) using BLAST [ 20] and SeqScape TM v 2.0 (Applied Biosystems, USA) software packages.
For this analysis, the putative ancestral P. falciparum allele for each SNP was determined by alignment with the reference genome sequence of the closely related chimpanzee parasite P. reichenowi CDC-1 strain54, with SNP positions being discarded if an ancestral allele was undetermined.
Sequence reads from repeat regions were identified by alignment with the reference chicken repeat sequences.
The presence or absence of the established NAI resistance-associated mutations, R292K and E119V, was then determined by inspection of the resulting amino acid alignment, with reference to the influenza A/Syd/5/97 (H3NA) NA sequence, which was isolated before the licensing and widespread use of neuraminidase inhibitors that began after 1999/2000.
DNA sequence conservation was assessed by alignment with the three orthologous primate reference sequences, viz., chimpanzee, gibbon, and rhesus.
Alignment with reference sequences and phylogenetic analyses were conducted by using MEGA 5.0 (5.0.
Five were classified as deletions based on sections of flanking sequence on at least one side of the Alu being deleted from the reference genome and by alignment with the chimpanzee genome [panTro4].
Mutations in the microsatellites among the inbred lines were identified by sequence alignment with the reference genome.
To assess the quality of FlexSnap alignment compared to other structural alignment methods, we evaluated the agreement of the methods' alignments with reference manually-curated alignments.
The gp60 allele and subtype were identified by multiple sequence alignment with GenBank reference sequences and phylogenetic analysis that used ClustalX version 1.8 (www.clustal.org) as well as manual quantification of microsatellite repeats.
