Sequence Logos

In 1990, Tom Schneider introduced Sequence logos as a way of graphically displaying consensus sequences. The characters representing the sequence are stacked on top of each other for each position in the aligned sequences. The height of each letter is made proportional to its frequency, and the letters are sorted so the most common one is on top. The height of the entire stack is then adjusted to signify the information content of the sequences at that position. From these ‘sequence logos’, one can determine not only the consensus sequence but also the relative frequency of bases and the information content (measured in bits) at every position in a site or sequence. The logo displays both significant residues and subtle sequence patterns (Nucleic Acids Res 1990;18:6097-100).

Sequence Logo graphic for a donor variant.

Creating Sequence Logos with vmvt

The following code creates a splice donor Logo.

import org.monarchinitiative.vmvt.core;

VmvtGenerator vmvt = new VmvtGenerator();
String donor = vmvt.getDonorLogoSvg();

A splice acceptor logo is created as follows.

import org.monarchinitiative.vmvt.core;

VmvtGenerator vmvt = new VmvtGenerator();
String donor = vmvt.getAcceptorLogoSvg();