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The resulting time series data were high-pass filtered with a default threshold of 128 s to remove low frequency drift.
In practice, it is computed using Q i = -10 log101 - 10- ms (i )/∑ i 10- ms (i ), with i looping over all the alignments of the insert of sufficiently high alignment score (with a default threshold of the 90th percentile of alignment scores computed for each read from bases of quality over 20).
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TFSEARCH http://www.cbrc.jp/research/db/TFSEARCH.html and TRANSFAC database [ 56], with a default threshold score of 85 were used for searching -400 bp 5' flanking region for possible transcription factors binding sites.
Blosum-62 matrix was used with a default threshold E-value of 10 and inclusion threshold value of 0.005.
A default threshold setting of 3 was used to reduce the chances of obtaining false positives.
Remaining species-specific intervening genes were finally compared to the NR nucleotide database of NCBI (release 10.5, ftp://ftp.ncbi.nih.gov) using Blastx tool [54], without filter of low complexity sequence, and with the default threshold of e-value of 10.
Applied to the same dataset, maSigPro selected 9374 and 2205 genes without thresholds on R2 and with the default threshold of 0.7, respectively.
Imputation parameters in Maskov were set to E = 5 with the default threshold of E, and the maximum amount of missing data set at seventy percent.
All enriched GO Terms were clustered into several functional groups by the functional annotation clustering method with the default threshold of enrichment score [ 30].
Peptides with no value for peak area (peak intensity below a default threshold in Libra) in any of the tagged channels were removed.
In ForC and ForJ a GBD was identified with confidence values slightly below the default threshold of the SMART tool.
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CEO of Professional Science Editing for Scientists @ prosciediting.com