Sequence rulers

Sequence rulers are SVG graphics that show the sequence of the donor or acceptor site, mark the intron-exon boundary, and show the position of any alternate bases that diverge from the reference sequence.

Donor ruler graphic

Sequence ruler graphic for a donor variant.

Creating Sequence Rulers with vmvt

The following code creates a splice donor ruler. 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.getDonorSequenceRuler(ref,alt);

The acceptor version is created analogously with the getAcceptorSequenceRuler command.