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.
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.