Conservation scores and constrained elements

We use GERP to calculate conservation scores and call constrained elements on the amniota vertebrate Pecan, mammals EPO_EXTENDED, fish EPO_EXTENDED and sauropsids EPO_EXTENDED multiple alignments. Calculation of these scores for different species groups allows the determination of regions that are conserved in one taxon but not another.

Conservation scores

Conservation scores are calculated per base, indicating how many species in a given multiple alignment match at each locus.

Constrained elements

Constrained elements are stretches of the multiple alignment where the sequences are highly conserved according to the previous score. This is calculated using GERP, which uses a permutation test to identify specific segments of the alignment that appear to be more conserved than expected by random chance. The p-values of constrained elements are calculated using a permutation test to generate new alignments which define the distribution of random expectation.