Sentence examples for using a reference sequence from inspiring English sources

Although we show results here using a reference sequence, this method, as the others, can be applied without a reference.

Using a reference sequence and comparing it with the query sequence, only the differences (i.e., variants) between the two are encoded into a VCF file.

Retained duplicate transcripts corresponding to isoflavone synthase/cellulose synthase, galactinol synthase, raffinose synthase and caffeoyl-CoA o-methyltransferase were identified with TBLASTX (default parameters) using a reference sequence against all soybean ESTs [ 58].

Exon/intron boundaries were identified using a reference sequence from A. burtoni (DQ386648) and checked by homology comparison with reference sequences from pufferfish (U63926), zebrafish (AF240639) and trout (AJ417832).

For the pooled exome sample, the alignment was performed using Novoalign using a reference sequence for the 165,637 bait intervals from the exome capture plus 76 bp flanking bases.

The genes within the cps loci that encoded proteins with the same homology group were assigned the same name, exceptions being those genes found in Region A. BLASTp (http://blast.ncbi.nlm.nih.gov/Blast.cgi PAGE=Proteins) searches were done by using a reference sequence database with default settings.

For these reasons at that time it was required to use a reference sequence coming from the assembly of multiple genomes.

Some published articles, however, use a reference sequence different from our selected reference sequence; in these cases, we respect the authors' choice by submitting the DNA change as described in those papers (Mank-Seymour, et al., 2006; Mohler, et al., 2007; Mohler, et al., 2004; Sherman, et al., 2005).

We start with remarking that we follow Engelhardt and Stephens (2010) to infer a SNP matrix from a dataset given in terms of a sequence of d ≥ 1 SNPs and n ≥ 1 accessions, that is, a d × n matrix whose entries are 0, 1, and 2. For this, we use a reference sequence and count for each locus of an accession the number of copies of the reference allele found at that locus.

The breseq pipeline uses a reference-sequence-based mapping strategy, which includes evaluating new sequence junctions supported by split-read alignments and tracking multiply-mapped reads, to predict point mutations and structural mutations from short-read DNA resequencing data.

These A. marginale sequencing reads were then used for a second Megablast alignment using as a reference sequence 28 nucleotides from the Himar1 terminal inverted repeats (TIR).