Exact(1)
BOOST achieves similar recall as STR but with substantially lower precision levels at both match thresholds.
Similar(59)
The topography is partitioned into "similar" and "dissimilar" peaks that meet or fall below the match threshold.
In all cases, FEX peak was defined as main peak since match angle was less than match threshold and also as a pure peak since purity angle was less than purity threshold under all forced tests.
In an alternative analysis, at the specified match threshold, the total number of binding sites in our set of promoters, before collapsing the overlaps, is 240160, while in a set of artificially generated sequences of the same length, there were 142202 matches.
A detailed example for a myocyte enhancer factor (MEF-2A), a mouse beta scaffold TF available retrieved from TRANSFAC public, is depicted in Figure 3. Three MEF isoforms from human are predicted by the respective beta scaffold SVR model to be highly similar to the PFM of the query factor and all lie above the required best match threshold of 0.95.
For each transcript, the top 10% of conserved regions in the 5000 bp up or down-stream sequences with minimum conservation of 70% and matrix match threshold of 80% were scanned for TFBS and the significance level was determined by Fisher's exact test score at p<0.05.
The matrix match threshold was 80% of the maximal match score.
If identities were still below the match threshold, the target sequences were compared with a second, third or fourth template.
Indeed, even NOWEI achieves higher recall and precision at match_thresh = 0.5, with a similar recall at the higher match threshold.
First, a cluster P is said to match a complex C at a given match threshold match_thres if Jaccard P, C) >= match_thres.
OrthoMCL was run with default settings, except for a percent match threshold of 35 and BLASTP set to print up to 10,000 alignments.
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