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Unexpectedly, the correlation between the number of miRNA sites and the conservation score of regions encompassing the coding region of genes was negative.
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The first layer is to compute the similarity score of region blocks and the second layer is a SVM classifier using HOG features.
If we ignore the position-specific effect and use the average conservation score of exon regions, upstream and downstream intronic regions, the error rate increases to 30.3%.
Several parameter that the MSER function takes will be explained: Delta: already mentioned in the MSER definition MaxVariation: defines the maximum variation (absolute stability score) of the regions MinDiversity: the minimum diversity of the region.
The median mapability score of all regions is 1 and the mean is 0.9930.
With this background distribution of the conservation score, we defined a functional human region as a conserved functional region if the conservation score of this region is within the top 3.5% of the background distribution.
For both constitutive exons and conditional exons, if the conservation score of exon region is high, the upstream intronic region is more conserved.
The concatenated feature vector is further fed into a hinge-loss SVM detector in a joint discriminative learning manner and the final saliency score of each region within the bounding box is obtained by the linear combination of the detector's weights.
Then, we calculate a saliency score of each region according to Eq. 10.
We call TNW l (n) the score of a region of n nucleotides which are adjacent to the right of the seed and which are computed with a PST l.
Shows mean scores and mean number of regions scoring above maximal consistent threshold for alignments containing 15, 14, 8 and 7 validated targets.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com