Sentence examples for using an alignment threshold from inspiring English sources

Using an alignment threshold of 80% identity over at least 80% of the query sequence and target size, approximately 4,200 homologous genes, present in both strains, were identified (4,183 CDS from STM 2683 presented at least one homolog in STM 4661 and 4,186 CDS from STM 4661 presented a minimum of one homolog in STM 2683).

The bam file produced for quantification were first filtered to eliminate poorly aligned sequences using an alignment quality threshold of 30 and a PCR duplicate filtering step (samtools v. 0.1.19-44428 cd).

An alignment threshold of 200 was used (−t 200), with adapter stripping (−a AGATCGGAAGAGCG) and quality calibration enabled (−k).

BLAST searches were performed using a significance threshold of an alignment length of >50 bp and an e-value of <10-4 (Additional file 3).

SAMtools [ 75] was used to call SNPs in the alignments using a coverage threshold of at least five reads overlapping a given SNP position and a minor allele frequency (MAF) for the SNP ≥ 0.05.

Alignments were filtered using an E-value threshold of 10-5, and the top KEGG protein hit for each transcript meeting the threshold was kept.

using an arbitrary threshold.

The blast hits were filtered using an e-value threshold of 10-5 and alignmentent length exceeding 80 bp.

Retrogenes containing Type III retrocopies were defined as having no significant BLAST alignment to any other protein coding genes (using an e-value threshold of 0.01).

(iii) Three additional sets of profiles were used in the case of mt336 alignment: 45 profiles defined using a different threshold on the UPGMA tree, the 25 stable profiles obtained from the analysis of the complete alignment, and the 20 profiles obtained by Le et al. [ 70].

Without using alignment thresholds, more than 99.9% of all sequences could be aligned back to the reference.