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Supplementary material for the article: Definition of supertypes for HLA molecules using clustering of specificity matrices.

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.

HLA-A logo's
HLA-B logo's
HLA-DR logo's
Furthermore er have included below links to the trees constructed using these specificity matrices
HLA-A tree
HLA-B tree
HLA-DR tree


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


References

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. Immunogenetics. abstract
Schneider TD, and Stephens RM. 1990. Sequence logos: a new way to display consensus sequences. Nucleic Acid Res 18: 6097-6100. abstract