The frequency characteristics of a low-pass and high-pass filter with matched cut-off frequencies are also complementary to one another (Fig. 5B).
OrthoMCL clustering analyses were performed using the following parameters: p-value cut-off = 1 × 10−5; Percent Identity cut-off = 0; Percent match cut-off = 80; MCL Inflation = 1.5; Maximum weight = 316.
Qualitative identification was performed using GC MS reference libraries (Adams [ 17], Wiley 7th, and NIST 2.0) using a 80% similarity match cut off value.
Peak identity was established by comparison of the fragmentation pattern with MS publicly available databases (NIST), using a match cut-off criterion of 750/1000 and by RI using the alkane series as standards.
Potential transcription factor binding sites in the human MER20-derived decidual PRL enhancer (dPRL) were identified using the MATCH program (http://.gene-regulation.com/) utilizing TRANSFAC binding site matrices with a match cut-off selected to minimize the sum of false positive and false negative results.
Four different match cut-off values for FACS were evaluated when using the mitochondrial reference (Supplementary Fig. 1).
Four different match cut-off values for FACS were evaluated when using the human reference (Supplementary Fig. 3).
Different match cut-off values were used with MEGABLAST to evaluate the reads classified with each method (Supplementary Fig. 2).
The match cut-offs were chosen based on their effect on the sensitivity and specificity of each method when trained on the synthetic metagenome dataset.
A sequence similarity of 45% with an alignment spanning over at least 45% of the query length served as a match cut-off for correct classification.
These homolog sequences accounted for <0.056% of all classified reads in the four K-mer sets with the different FACS match cut-off values.
