Sentence examples for a stringency set from inspiring English sources
Moreover, we also did TBLASTN searches of frog EST data against the Xenopus Genome EST databases with a stringency set as E ≤ 0.0001 and an identity of 90% or higher as candidacy.
Whole genome sequence comparisons were performed using CoreGenes with a stringency setting of 75 http://www.binf.gmu.edu/genometools.html[ 96, 34].
A large part (42.6%) of the LXR binding locations in the high stringency set represent the well understood case of LXR being present on its genomic binding site both before and after the ligand treatment.
On the other hand, for the high stringency set we accepted only 1 median false positive.
Annotation clustering was performed with stringency set to "high".
Parameters for the assembly were set to high stringency: vector scanning, 32bp trimming of all 5' ends, minimum Phred score of 20, minimum length of matching word increased to 30, and level of contigs merging stringency set to the highest.
At the stringency set for this search, neither the upstream NF-κB element nor the putative ISRE sequences at −952/−940 and −924/−911 showed up as consensus elements, consistent with weak STAT1 binding.
Results with ANT3 models (Additional files 4 and 5): no candidate genes were identified with regular stringency (set as the same level of that used for the three other ANT sequences).
Functional annotation of genes was assessed using DAVID Bioinformatics Resources v6.7 [ 54], specifically the functional annotation clustering enrichment threshold for EASE was set to 1.3 with stringency set to HIGH; from the resulting clusters only those with an enrichment score ≥ 1.3 (P < 0.05) were retained.
Compared to the assemblies generated with our optimized Phrap parameters, those generated using the 'repeat stringency' set at 99 or 'shatter greedy' were inferior with respect to the above measures, and would have required substantial additional effort to complete the finishing process.
Finally, 15-way orthologous gene alignments were constructed with a high conservation stringency setting (connectivity cutoff = 0.5) in Proteinortho for the following phylogenetic analysis.
