Sequence trekkers

We combine the sequence logo (see Sequence Logos) and walker (see Sequence walkers) in a new figure that we call sequence trekker (because a trek goes further than a walk).

Sequence Trekker graphic for a +1G>A donor variant.

Creating Sequence Trekkers with vmvt

The following code creates a splice donor walker. 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.getDonorTrekkerSvg(ref,alt);