Delta Ri Score

The individual sequence information of a sequence and an alternate sequence are showing using the Sequence Walker (see Sequence walkers). This graphic shows the value of the difference between the reference sequence and an alternate sequence as well as the distribution of random changes to sequences of the same length. A variant that reduces the sequence information is associated with a positive delta-Ri score.

Delta graphic for a +1 donor variant.

Creating Delta Plots with vmvt

The following code creates a delta plot. Note that the input Strings must be 9 nucleotides long. Vmvt will treat the string as corresponding to positions (-3,+6) of the intron-exon boundary of a splice donor sequence. Sequences can be provided in upper or lower case.

import org.monarchinitiative.vmvt.core;

final String ref = "AAGGTCAGA";
final String alt = "AAGATCAGA";

VmvtGenerator vmvt = new VmvtGenerator();
String svg = vmvt.getDelta(ref,alt);

The command works for both donor and acceptor sequences (the code figures out if the sequences passed to it are donor sequences (i.e., 9 nt) or acceptor sequences (i.e., 27 nt).