Supplementary material for the article:
Definition of supertypes for HLA molecules using clustering of specificity
In the article we visualize the characteristics of the different binding
motifs using the logo program (Schneider, 1990). To be able to see the
logo's more clearly we have put them here as supplementary material.
Furthermore er have included below links to the trees constructed using these
Explanation of the logo visualization
The information content at each
position in the sequence motif corresponds to the height of a
column of letters. The Information content Ip on each position
p is defined as log2(20) + Σa(pap log2(pap)).
The information content is a measure of the degree of conservation
and lies within the range of 0 (no conservation-all amino acids
are equally probable) and
log2(20) = 4.3 (full conservation-only a single amino acid is
observed at that position).
The height of each letter within the columns is proportional to the
frequency pap of the corresponding amino acid a at that position p.
The amino acids are colored according to their properties:
- Acidic [DE] red
- Basic [HKR]: blue
- Hydrophobic: [ACFILMPVW] black
- Neutral [GNQSTY]: green
Lund O, Nielsen M, Kesmir C, Petersen AG, Lundegaard C, Worning P, Sylvester-Hvid C, Lamberth K, Roder G, Justesen S, Buus S, Brunak S.
Definition of supertypes for HLA molecules using clustering of specificity matrices.
Schneider TD, and Stephens RM. 1990. Sequence logos:
a new way to display consensus sequences. Nucleic Acid Res 18: 6097-6100.