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SIFT makes use of sequence homology and median evolutionary conservation scores to predict conserved protein function.
The conservation scores were predicted based on non-conserved and conserved models.
Conservation scores can be considered as probabilities that each SNP lies in a conserved element [48].
Genome conservation scores (phastcons) and ENCODE peaks were retrieved from the UCSC browser using rtracklayer [64,65].
PhastCons conservation scores were downloaded from the UCSC download pages.
Conservation scores were assigned to every position of those fragments.
Some of the conditional exons have high conservation scores and some of them have very low conservation scores (Fig. 4A).
Some of the conditional exons have high conservation scores and some of them have very low conservation scores.
Base-by-base conservation scores for human bases were downloaded from UCSC Conservation Track [47] which used phastCons [48] to calculate conservation scores across 28 mammalian species.
There are dramatic differences in conservation scores between conditional exons and constitutive exons.
Figure 2A plots conservation scores along relative positions of exons or introns.
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